🧬 hotSpring CompChem GuideStone
Computational chemistry validation — free energy landscapes via well-tempered metadynamics
Domain Profile
This pseudoSpore validates computational chemistry methods for carbohydrate conformational analysis. It reproduces free energy landscapes (FELs) for xylose ring puckering in enzyme-bound and free states using well-tempered metadynamics with GROMACS/PLUMED.
The guideStone verification class ensures that every energy surface can be independently re-derived from raw simulation data using documented commands.
Module Status
| # | Module | Collective Variables | Duration | Status |
|---|---|---|---|---|
| 1 | Alanine dipeptide FEL | φ/ψ 2D Ramachandran | 10 ns | PASS |
| 2 | Xylose puckering (free) | θ 1D Cremer-Pople | 10 ns | PASS |
| 3 | Enzyme-bound puckering | θ 1D Cremer-Pople | 10 ns | PASS |
| 4 | Free xylose 2D | qx, qy 2D Cremer-Pople | 20 ns | PASS |
| 5 | Enzyme-bound 2D | qx, qy 2D Cremer-Pople | 20 ns | PASS |
| 6 | Cross-tier parity | Rust vs Python (all) | — | PASS |
| 7 | Convergence analysis | Block averaging | — | PASS |
| 8 | GPU parity | barraCuda vs CPU | — | PENDING |
7 of 8 modules passing. Module 8 (GPU parity) awaits barraCuda FEL kernel deployment.
Provenance
| Property | Value |
|---|---|
| Origin | ecoPrimals/springs/hotSpring |
| Version | 1.6.1 |
| Spring | hotSpring |
| Emission method | litho emit-pseudospore |
| Integrity | BLAKE3 checksums in receipts/checksums.blake3 |
| Braid | FermentBraid provenance chain (who/what/when/how) |
Zero-Trust Derivation
Every output in this pseudoSpore can be independently verified:
# Extract and verify checksums
cd pseudoSpore_hotSpring-CompChem-GuideStone_v1.6.1/
b3sum --check receipts/checksums.blake3
# Re-derive a free energy surface from raw HILLS data
plumed sum_hills --hills data/xylose-puckering-fel/HILLS \
--mintozero --outfile /tmp/fes_theta.dat
diff outputs/xylose-puckering-fel/fes_theta.dat /tmp/fes_theta.datTier Parity
| Tier | Implementation | Role |
|---|---|---|
| Tier 1 | Python (NumPy/SciPy) | Golden reference values |
| Tier 2 | Rust (hotSpring binary) | Production validator |
| Tier 3 | WGSL (barraCuda kernel) | GPU-accelerated (pending) |
Cross-tier RMSD tolerances: < 1.0 kJ/mol for 1D, < 2.0 kJ/mol for 2D surfaces.
Download
The lithoSpore archive contains all raw data, configurations, outputs, and verification scripts needed to independently reproduce every result.
Archive: pseudoSpore_hotSpring-CompChem-GuideStone_v1.6.1.tar.gz Verify: litho ingest-pseudospore <path> --verify