{
  "schema": "dia-health-one.engine-preflight.v1",
  "run": {
    "id": "DHO-ENGINE-PREFLIGHT-20261017T190112Z",
    "started_at_utc": "2026-10-17T18:58:25.575271+00:00",
    "completed_at_utc": "2026-10-17T19:01:12.750881+00:00",
    "script_sha256": "3477240e0f8f82dd43893a56e18eb7ff999bb5eb1ec92903b9dee0293e4fccf9",
    "input_sha256": "d4a6812d8951cf6594e6a0763f089e35f5a80b62acb3c117b2c5565228a7b161",
    "software_environment": "research/engine-benchmark-environment.yml",
    "python_version": "3.13.16",
    "host_os": "macOS-26.3-arm64-arm-64bit-Mach-O",
    "host_architecture": "arm64",
    "host_processor": "Apple M4",
    "nvidia_gpu_available": false,
    "nvidia_gpu_used": false,
    "clinical_use": false
  },
  "source_system": {
    "structure_id": "1UBQ",
    "source_url": "https://www.rcsb.org/structure/1UBQ",
    "structure_class": "public experimental X-ray structure of ubiquitin",
    "protein_residues": 76,
    "force_field": "Amber99SB-ILDN",
    "water_model": "TIP3P",
    "water_box_coordinates": "GROMACS spc216.gro three-site water coordinates",
    "box_padding_nm": 1.0,
    "added_salt": false,
    "solvated_atom_count": 26821
  },
  "protocol": {
    "purpose": "engine throughput and installation preflight only",
    "timed_steps": 5000,
    "openmm_warmup_steps_excluded_from_timing": 500,
    "timestep_ps": 0.002,
    "temperature_K": 300.0,
    "random_seed": 1729,
    "threads": 4,
    "gromacs_integrator": "md with v-rescale thermostat",
    "openmm_integrator": "LangevinMiddleIntegrator",
    "limitations": [
      "One short run per engine/platform; timing is not a statistically sampled benchmark.",
      "GROMACS and OpenMM use different thermostat implementations.",
      "GROMACS mdrun timing includes run setup; OpenMM timing excludes setup, minimization, and warmup.",
      "The test protein is not NNC2215, PaG, or an insulin-receptor complex.",
      "The OpenCL result is from Apple M4 hardware, not an NVIDIA GPU.",
      "Throughput does not validate force-field quality or predict binding affinity."
    ]
  },
  "available_openmm_platforms": [
    {
      "platform": "CPU",
      "available": true
    },
    {
      "platform": "OpenCL",
      "available": true
    }
  ],
  "measurements": [
    {
      "engine": "GROMACS",
      "version": "2026.3-conda_forge",
      "platform": "CPU",
      "threads": 4,
      "gpu_support_in_build": false,
      "steps": 5000,
      "timestep_ps": 0.002,
      "ns_per_day": 37.42,
      "hours_per_ns": 0.641,
      "milliseconds_per_step": 4.618,
      "million_atom_steps_per_second": 5.808,
      "minimization_steps": 734,
      "solvated_atom_count": 26821,
      "timing_note": "GROMACS mdrun-reported wall time, including engine run setup."
    },
    {
      "engine": "OpenMM",
      "version": "8.6.1",
      "platform": "CPU",
      "platform_properties": {
        "Threads": "4",
        "DeterministicForces": "true"
      },
      "threads": 4,
      "steps": 5000,
      "warmup_steps_excluded_from_timing": 500,
      "timestep_ps": 0.002,
      "timed_seconds": 77.55086,
      "ns_per_day": 11.141,
      "million_atom_steps_per_second": 1.729,
      "solvated_atom_count": 26821,
      "initial_potential_energy_kj_mol_after_warmup": -378333.184,
      "timing_note": "OpenMM wall time for production steps only, after 500 warmup steps; setup and minimization excluded."
    },
    {
      "engine": "OpenMM",
      "version": "8.6.1",
      "platform": "OpenCL",
      "platform_properties": {
        "Precision": "single",
        "DeviceIndex": "0"
      },
      "threads": null,
      "steps": 5000,
      "warmup_steps_excluded_from_timing": 500,
      "timestep_ps": 0.002,
      "timed_seconds": 6.84229,
      "ns_per_day": 126.274,
      "million_atom_steps_per_second": 19.599,
      "solvated_atom_count": 26821,
      "initial_potential_energy_kj_mol_after_warmup": -379214.31,
      "timing_note": "OpenMM wall time for production steps only, after 500 warmup steps; setup and minimization excluded."
    }
  ],
  "interpretation": {
    "status": "local generic engine preflight complete",
    "target_nnc2215_pag_md_run": false,
    "nvidia_acceleration_demonstrated": false,
    "scale_up_recommendation": "Repeat a controlled benchmark on the allocated NVIDIA system; do not use this preflight to select production MD parameters or infer NNC2215/PaG energetics."
  }
}