v1 · compute gate

MD Smoke v1

The first molecular-dynamics compute contract for TWOG: expert-reviewed inputs, small smoke settings, structured worker diagnostics, and ledgered artifacts.

operator-gatedapplies to · Modal MD smoke jobsclaims · workflow proof
What this governs

MD Smoke v1 proves that TWOG can submit, track, and inspect a molecular-dynamics style job. It does not prove a molecule works.

GPU work is approval-first, ledgered, and treated as workflow evidence until stronger science is attached.

01 · Input packet

The job requires protein PDB text, compound SMILES, target and compound names, simulation steps, temperature, and provenance for protein and ligand preparation.

02 · Expert gate

A review packet checks whether the inputs and assumptions are suitable for a smoke run before live compute is allowed.

03 · Worker execution

The Modal GPU worker validates inputs, prepares protein and ligand artifacts, runs the enabled smoke stages, and returns structured stage diagnostics.

04 · Ledger

Provider job IDs, worker outputs, stage errors, artifacts, cost fields, and status transitions are persisted in the TWOG compute ledger.

05 · Record attachment

A candidate can link to compute evidence only as an inspectable artifact, with clear limits on what the smoke result does and does not show.

What smoke means

A smoke run is a systems test. It checks that the compute path, inputs, worker image, diagnostics, and artifact handling behave correctly.

What it does not mean

A smoke run is not a binding claim, efficacy claim, dosing claim, or safety claim. It is not a substitute for docking validation, long MD, free energy analysis, or wet-lab work.

Why ligand prep matters

The worker preserves ligand chemistry from SMILES through RDKit-based 3D generation before conversion into downstream formats, instead of relying on a lossy PDB-only ligand intermediate.

Why structured failures matter

A failed worker run is useful when the stage, command, return code, stdout tail, stderr tail, and payload are persisted. Opaque failures are treated as worker defects.

What a reader can verify
Inputs
Protein source, ligand source, SMILES, PDB validation, simulation settings, and preparation method.
Approval
Expert approval metadata tied to the exact packet version.
Worker stages
Input validation, protein prep, ligand 3D, ligand PDBQT, docking, MD smoke, warnings, and errors.
Artifacts
Sanitized PDB, ligand files, output payloads, plots, and hashes when available.
Cost and status
Provider job ID, status, timestamps, runner profile, and any cost estimates or actuals.
How to interpret this method
  • Successful smoke means the compute lane worked, not that the candidate is validated.
  • Failed smoke can still improve the worker if it returns structured diagnostics.
  • No public contribution should launch MD directly.
  • Every compute result needs a method reference and ledger ID before it belongs on a candidate page.
What this method does not certify

MD Smoke v1 is a compute-contract method. Scientific interpretation requires additional validated protocols, controls, replication, and expert review.