OpenFE RBFE - jacs_set - thrombin, tyk2 - 2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p

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 (thrombin, tyk2)prepared with ff14SB/lipid17_merged/phosaa10/tip3p_HFE_multivalent/tip3p_standard 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 72 edges across 27 unique ligands. Results are derived from archivedAlchemiscale workflow data. For scripts to generate this network:github.com/openforcefield/alchemical-benchmark-resources/submissions/2026_07_23_ff14sb_openff-3.0.0-alpha1b_tip3p/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_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin Software Versionsopenfe_version: "1.8.0"openmm_version: "8.2.0"openff_toolkit_version: "0.18" Alchemical Network Keys - AlchemicalNetwork-8f0230086292763f9be6b738348307e8: jacs_set/thrombin - AlchemicalNetwork-a1efafd1298d735c7032cebe52be9665: jacs_set/tyk2 Recommended Descriptorsforcefield: ["ff14SB", "lipid17_merged", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"]small_molecule_forcefield: "openff-3.0.0-alpha1b"partial_charges: nagl_openff-gnn-am1bcc-1.0.0.ptmapper: "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": "thrombin": AlchemicalNetwork-8f0230086292763f9be6b738348307e8 "tyk2": AlchemicalNetwork-a1efafd1298d735c7032cebe52be9665 Protocol Settingsprotocol_settings: - protocol: "RelativeHybridTopologyProtocol" protocol_library: "openfe" timestep: "4.0 fs" temperature: "298.15 K" pressure: "1 bar" forcefields: ["ff14SB", "lipid17_merged", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"] 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 36 edges: - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=1c, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=3b, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=5, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1b, ligand_final=1a, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1d, ligand_final=1b, solvent={'O'}, cofactors=none, protein={'unknown'} - etc. - protocol: "RelativeHybridTopologyProtocol" notes: | Detailed protocol settings differ: - solvation_settings.solvent_padding: 1 -> 1.5 Applies to 36 edges: - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=1c, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=3b, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1a, ligand_final=5, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1b, ligand_final=1a, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-8f0230086292763f9be6b738348307e8 jacs_set-thrombin: ligand_start=1d, ligand_final=1b, solvent={'O'}, cofactors=none, protein=none - etc.