OpenFE RBFE - jacs_set - tyk2 - 2026-06-22-tyk2-alchemicalarchive-test

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 (tyk2) prepared with ff14SB/phosaa10/tip3p_HFE_multivalent/tip3p_standard for proteins and solvents, and openff-2.3.0 with nagl_openff-gnn-am1bcc-1.0.0.pt for ligands, solutes, and cofactors. The network contains 44 edges across 16 unique ligands. Results are derived from archived Alchemiscale workflow data. This subset of the JACS set is meant to provide an example of an alchemical archive submission and provide an indication of the variability in results. For scripts to generate this network: github.com/openforcefield/alchemical-benchmark- resources/submissions/2026_03_17_openff-2.3.0_jacs_tyk2/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/2026-06-22-tyk2-alchemicalarchive-test Software versions openfe_version: 1.8.0 openmm_version: 8.2.0openff_toolkit_version: 0.18 Alchemical Network Keys - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d: jacs_set/tyk2 Recommended Descriptors forcefield: ["ff14SB", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"] small_molecule_forcefield: "openff-2.3.0" 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": "tyk2": AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d Protocol Settings protocol_settings: protocol: "RelativeHybridTopologyProtocol"timestep: "4.0 fs"temperature: "298.15 K"pressure: "1 bar"forcefields: ["ff14SB", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"]small_molecule_forcefield: "openff-2.3.0"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 12 edges: - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_31, ligand_final=none, solvent=none, cofactors=none, protein=none - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_42, ligand_final=none, solvent=none, cofactors=none, protein=none - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_43, ligand_final=none, solvent=none, cofactors=none, protein=none - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_44, ligand_final=none, solvent=none, cofactors=none, protein=none - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_47, ligand_final=none, solvent=none, cofactors=none, protein=none - etc. protocol: "RelativeHybridTopologyProtocol"notes: | Detailed protocol settings differ: - solvation_settings.solvent_padding: 1.5 -> 1 Applies to 12 edges: - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_31, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_42, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}= - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_43, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_44, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2dd5d032b0228c7474eda50d8e064c2d jacs_set-tyk2: ligand_start=ejm_47, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'} - etc.