diff --git a/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/computational_results.json.bz2 b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/computational_results.json.bz2 new file mode 100644 index 0000000..ffd017b Binary files /dev/null and b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/computational_results.json.bz2 differ diff --git a/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/submission.yaml b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/submission.yaml new file mode 100644 index 0000000..94ff973 --- /dev/null +++ b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/submission.yaml @@ -0,0 +1,97 @@ +# REQUIRED: unique, kebab-case identifier for this submission +submission_id: 2026_08_05_openff-3.0.0-alpha0_opc3_jacs + +# REQUIRED: short descriptive title +title: OpenFE RBFE - jacs_set (8 systems) - 2026_08_05_openff-3.0.0-alpha0_opc3_jacs + +# REQUIRED: short descriptive summary (1-2 sentences) +summary: | + 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-alpha0 for proteins and + solvents, and openff-3.0.0-alpha0 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_23_openff-3.0.0-alpha0_opc3/alchemiscale_submission.ipynb + +# REQUIRED: list of submission tags +tags: [rbfe, opc3.offxml, openff-3.0.0-alpha0, bace, cdk2, jacs_set, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe] + +# REQUIRED: list of contributing authors (name, affiliation; ORCID optional) +authors: + - name: Jennifer A. Clark + +# REQUIRED: publication/submission date (ISO 8601) +date: 2026-08-05 +openfe_version: "1.8.0" +openmm_version: "8.2.0" +openff_toolkit_version: "0.18" +mapper: "KartografAtomMapper 1.2.0 (LSA)" +forcefield: ["opc3.offxml", "openff-3.0.0-alpha0"] +small_molecule_forcefield: "openff-3.0.0-alpha0" +partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt" + +## 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-0482bbeceac4470dd4c29afeadfa5825 + "cdk2": AlchemicalNetwork-ea875d9e2896b0e337a17bf950c722ba + "jnk1": AlchemicalNetwork-7420dd6f7be012084483a3d57faa2350 + "mcl1": AlchemicalNetwork-21aba16db838ca5833ad036c37ee50d2 + "p38": AlchemicalNetwork-ff43514f04705b71bcb834c34c8e51b0 + "ptp1b": AlchemicalNetwork-c7614ad07bf6ffffd3369475e628e20e + "thrombin": AlchemicalNetwork-febece7a6c1eb4f964a57f994934a31a + "tyk2": AlchemicalNetwork-ea6d43b749172c8d7df19a66bec9838a + + +# REQUIRED: results file +results: computational_results.json.bz2 + +# REQUIRED: long-term archive pointer (at least doi or url) +archive: + doi: 10.5281/zenodo.21810556 + archive_provider: zenodo + +# REQUIRED: license for the submission +license: CC-BY-4.0 + +# RECOMMENDED / OPTIONAL metadata for protocol settings +protocol_settings: + - protocol: "HybridTopProtocol" + protocol_library: "pontibus" + timestep: "4.0 fs" + temperature: "298.15 K" + pressure: "1 bar" + forcefields: ["opc3.offxml", "openff-3.0.0-alpha0"] + small_molecule_forcefield: "openff-3.0.0-alpha0" + 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-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13c, solvent={'O'}, cofactors=none, protein={'unknown'} + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13f, solvent={'O'}, cofactors=none, protein={'unknown'} + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13g, solvent={'O'}, cofactors=none, protein={'unknown'} + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13i, solvent={'O'}, cofactors=none, protein={'unknown'} + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13o, 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-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13c, solvent={'O'}, cofactors=none, protein=none + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13f, solvent={'O'}, cofactors=none, protein=none + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13g, solvent={'O'}, cofactors=none, protein=none + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13i, solvent={'O'}, cofactors=none, protein=none + - AlchemicalNetwork-0482bbeceac4470dd4c29afeadfa5825 jacs_set-bace: ligand_start=CAT-13a, ligand_final=CAT-13o, solvent={'O'}, cofactors=none, protein=none + - etc. + diff --git a/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/computational_results.json.bz2 b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/computational_results.json.bz2 new file mode 100644 index 0000000..e383f63 Binary files /dev/null and b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/computational_results.json.bz2 differ diff --git a/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/submission.yaml b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/submission.yaml new file mode 100644 index 0000000..ff87303 --- /dev/null +++ b/openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/submission.yaml @@ -0,0 +1,97 @@ +# REQUIRED: unique, kebab-case identifier for this submission +submission_id: 2026-08-05-openff3.0.0-alpha1b_tip3p-jacs + +# REQUIRED: short descriptive title +title: OpenFE RBFE - jacs_set (8 systems) - 2026-08-05-openff3.0.0-alpha1b_tip3p-jacs + +# REQUIRED: short descriptive summary (1-2 sentences) +summary: | + 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 + +# REQUIRED: list of submission tags +tags: [rbfe, openff-3.0.0-alpha1b, tip3p.offxml, bace, cdk2, jacs_set, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe] + +# REQUIRED: list of contributing authors (name, affiliation; ORCID optional) +authors: + - name: Jennifer A. Clark + +# REQUIRED: publication/submission date (ISO 8601) +date: 2026-08-05 +openfe_version: "1.8.0" +openmm_version: "8.2.0" +openff_toolkit_version: "0.18" +mapper: "KartografAtomMapper 1.2.0 (LSA)" +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" + +# 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 + + +# REQUIRED: results file +results: computational_results.json.bz2 + +# REQUIRED: long-term archive pointer (at least doi or url) +archive: + doi: 10.5281/zenodo.21809947 + archive_provider: zenodo + +# REQUIRED: license for the submission +license: CC-BY-4.0 + +# RECOMMENDED / OPTIONAL metadata for protocol settings +protocol_settings: + - protocol: "HybridTopProtocol" + protocol_library: "pontibus" + timestep: "4.0 fs" + temperature: "298.15 K" + pressure: "1 bar" + forcefields: ["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" + 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. + diff --git a/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/computational_results.json.bz2 b/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/computational_results.json.bz2 new file mode 100644 index 0000000..4cd653a Binary files /dev/null and b/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/computational_results.json.bz2 differ diff --git a/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/submission.yaml b/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/submission.yaml new file mode 100644 index 0000000..76fa967 --- /dev/null +++ b/openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/submission.yaml @@ -0,0 +1,91 @@ +# REQUIRED: unique, kebab-case identifier for this submission +submission_id: 2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin + +# REQUIRED: short descriptive title +title: OpenFE RBFE - jacs_set - thrombin, tyk2 - 2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin + +# REQUIRED: short descriptive summary (1-2 sentences) +summary: | + 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 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 72 edges across 27 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_23_ff14sb_openff-3.0.0-alpha1b_tip3p/alchemiscale_submission.ipynb + +# REQUIRED: list of submission tags +tags: [rbfe, ff14SB, lipid17_merged, phosaa10, tip3p_HFE_multivalent, tip3p_standard, openff-3.0.0-alpha1b, jacs_set, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, benchmark, openfe] + +# REQUIRED: list of contributing authors (name, affiliation; ORCID optional) +authors: + - name: Jennifer A. Clark + +# REQUIRED: publication/submission date (ISO 8601) +date: 2026-08-05 +openfe_version: "1.8.0" +openmm_version: "8.2.0" +openff_toolkit_version: "0.18" +mapper: "KartografAtomMapper 1.2.0 (LSA)" +forcefield: ["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.pt" + +## 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 + + +# REQUIRED: results file +results: computational_results.json.bz2 + +# REQUIRED: long-term archive pointer (at least doi or url) +archive: + doi: 10.5281/zenodo.21810274 + archive_provider: zenodo + +# REQUIRED: license for the submission +license: CC-BY-4.0 + +# RECOMMENDED / OPTIONAL metadata for protocol settings +protocol_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: "openff-3.0.0-alpha1b" + 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. +