2026-03-18-openmm-840-qa-testing

RBFE benchmark results prepared from AlchemicalNetwork JSON file(s) generated with OpenFE.

This submission describes QA testing using openmm-8.4 with the charge_annihilation_set and jacs_set RBFE benchmark (charge_annihilation_set: egfr, irak4_s2, irak4_s3; jacs_set: p38, tyk2) prepared with openfe-benchmarks.

 

The submission uses the openff-2.3.0 small molecule force field and nagl_openff-gnn-am1bcc-1.0.0.pt charge model and contains 160 transformations, 61 unique ligands, and 5 unique proteins. The largest simulated chemical system contains 6744 atoms. Note this means the charge annihilation sets are not complete compared to what is in that system and should not be compared to other complete runs due to the missing edges.

 

This submission was run locally on HPC3 and so no AlchemicalArchive is available, but the raw outputs are included.

- openfe_version: 1.9.1

- openmm_version: 8.4.0

- openff_toolkit_version: 0.18.0

  - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191: jacs_set/p38
  - AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a: charge_annihilation_set/irak4_s3
  - AlchemicalNetwork-b15bcfadae8a358cee9a7dcb9f5445d6: charge_annihilation_set/egfr
  - AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9: charge_annihilation_set/irak4_s2
  - AlchemicalNetwork-ed08b22af2e51875d23b0283d2080252: jacs_set/tyk2

- forcefield: openff-2.3.0

- partial_charges: nagl_openff-gnn-am1bcc-1.0.0.pt

- forcefield: ["ff14SB", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"]
- small_molecule_forcefield: "openff-2.3.0"
- mapper: "KartografAtomMapper 1.2.0 (LSA)"

  source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks
  "charge_annihilation_set":
    "egfr": AlchemicalNetwork-b15bcfadae8a358cee9a7dcb9f5445d6
    "irak4_s2": AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9
    "irak4_s3": AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a
  "jacs_set":
    "p38": AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191
    "tyk2": AlchemicalNetwork-ed08b22af2e51875d23b0283d2080252

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: "am1bcc_at"
    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 40 edges:
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2bb, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2c, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2ee, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2f, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - etc.
  - protocol: "RelativeHybridTopologyProtocol"
    production_time: "20 ns"
    lambda_windows: "22"
    notes: |
      Detailed protocol settings differ:
      - alchemical_settings.explicit_charge_correction: False -> True
      - lambda_settings.lambda_windows: 11 -> 22
      - simulation_settings.n_replicas: 11 -> 22
      - simulation_settings.production_length: 5.0 -> 20
      - solvation_settings.solvent_padding: 1 -> 1.5
      Applies to 5 edges:
      - AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a charge_annihilation_set-irak4_s3: ligand_start=19charg, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a charge_annihilation_set-irak4_s3: ligand_start=28charg, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-b15bcfadae8a358cee9a7dcb9f5445d6 charge_annihilation_set-egfr: ligand_start=21, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9 charge_annihilation_set-irak4_s2: ligand_start=17charg, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9 charge_annihilation_set-irak4_s2: ligand_start=6, ligand_final=none, solvent=none, cofactors=none, protein=none
  - protocol: "RelativeHybridTopologyProtocol"
    production_time: "20 ns"
    lambda_windows: "22"
    notes: |
      Detailed protocol settings differ:
      - alchemical_settings.explicit_charge_correction: False -> True
      - lambda_settings.lambda_windows: 11 -> 22
      - simulation_settings.n_replicas: 11 -> 22
      - simulation_settings.production_length: 5.0 -> 20
      Applies to 5 edges:
      - AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a charge_annihilation_set-irak4_s3: ligand_start=19charg, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-6c2af871ad714bf6cda4368eb34fd06a charge_annihilation_set-irak4_s3: ligand_start=28charg, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-b15bcfadae8a358cee9a7dcb9f5445d6 charge_annihilation_set-egfr: ligand_start=21, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9 charge_annihilation_set-irak4_s2: ligand_start=17charg, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
      - AlchemicalNetwork-e516aadebadf1c036b5930cf7838c6d9 charge_annihilation_set-irak4_s2: ligand_start=6, ligand_final=none, solvent=none, cofactors=none, protein={'unknown'}
  - protocol: "RelativeHybridTopologyProtocol"
    notes: |
      Detailed protocol settings differ:
      - solvation_settings.solvent_padding: 1 -> 1.5
      Applies to 40 edges:
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2bb, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2c, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2ee, ligand_final=none, solvent=none, cofactors=none, protein=none
      - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2f, ligand_final=none, solvent=none, cofactors=none, protein=none
      - etc.

Rights

- License: CC-BY-4.0