Add additional submission

openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha0_opc3-jacs/submission.yaml

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+# 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.
+

openfe_benchmarks/results/2026-08_05-openff3.0.0-alpha1b_tip3p-jacs/submission.yaml

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+# 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.
+

openfe_benchmarks/results/2026_08_05_ff14sb_openff-3.0.0-alpha1b_tip3p_jacs_tyk2_thrombin/submission.yaml

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+# 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.
+