SciDEX — Task: [Forge] End-to-end MD-simulation analysis

Composes molecular-dynamics skill into a production MD pipeline with RMSF/PCA/HBond analysis and Skeptic-prompt injection.

Completion Notes

Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle

Spec File

Effort: extensive

Goal

Compose the molecular-dynamics skill (OpenMM + MDAnalysis) into a production MD pipeline: given a structure (PDB id, AlphaFold
prediction, or docking-output complex), prepare the system with
appropriate force fields, run a configurable production simulation
(default 100 ns), analyze the trajectory for RMSF, dynamic cross-
correlation, principal-component motion modes, and persist all
outputs as a versioned MD-run artifact. Used by Theorist to ground
"protein dynamics" claims in actual simulation, not literature
hand-waving.

Why this matters

The molecular-dynamics skill exists (.claude/skills/molecular-dynamics)
but no Forge tool composes it into a hypothesis-grounding workflow.
A debate over "this loop is conformationally flexible and that's why
the drug doesn't bind well" needs MD evidence to settle; today the
Skeptic has no way to demand it. A reproducible MD pipeline turns
this from a literature-citation contest into an experimental-evidence
exchange — a much higher epistemic bar.

Acceptance Criteria

☐ New module scidex/forge/md_pipeline.py (≤900 LoC):

prepare_system(structure, force_field='amber14',
        water_model='tip3p', ions='0.15 M NaCl')

— uses OpenMM's
Modeller to add hydrogens, solvate, neutralize; returns
system, topology, positions.
-

run_production(system, topology, positions, ns=100,
        timestep_fs=2.0)

— runs production MD with a Langevin
integrator at 310 K; periodic checkpointing so partial
runs are recoverable.
- analyze_trajectory(traj_path) — uses MDAnalysis to compute
RMSF per residue, dynamic cross-correlation matrix, PCA on
Cα coordinates yielding top-5 motion modes, hydrogen-bond
occupancy, secondary-structure flips.
- pipeline(structure_or_pdb_id, ns=100) — composes; commits
outputs to data/scidex-artifacts/md/<structure>/<run_id>/
including the trajectory (xtc), the analysis JSON, and
SVG plots for each metric.

☐ Migration md_run(run_id PRIMARY KEY, structure_source,


      pdb_id_or_artifact_id, force_field, water_model, ions, length_ns,
      timestep_fs, n_atoms, runtime_seconds, mean_rmsf, top_pca_variance,
      hardware_profile, started_at, finished_at, artifact_id)

☐ tools.py registers md_simulation_pipeline(pdb_id, ns=100)

with @log_tool_call; default ns is 100; CPU runs hard-cap at
10 ns to prevent runaway.

☐ /artifacts/<id> renders RMSF plot, top-3 PCA motion-mode

animations (GIF), and a residue-flexibility heatmap.

☐ Skeptic persona prompt gains an md_evidence block when the

hypothesis names a protein with a completed MD run (mean RMSF +
top-PCA variance summary).

☐ Acceptance: python -m scidex.forge.md_pipeline --pdb 1AKI --ns

(lysozyme, fast control) completes <30 min on the build
host; mean RMSF in expected range (1-3 Å for the loop region);
artifact registered.

☐ Resource governance: get-available-resources queried before

run; refuses if estimated runtime > 24 h or RAM < 8 GB.