coarse-grained — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited coarse-grained (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
Run µs–ms scale MD simulations using coarse-grained force fields. Primary use cases: membrane self-assembly, protein-membrane interactions, lipid nanoparticles, large conformational changes, crowding effects.
| File | Content |
|---|---|
references/cg-theory.md | CG resolution levels, mapping schemes, Boltzmann inversion, force matching, MARTINI 3 philosophy, bead types, scaling factors |
references/martini-proteins.md | martinize2, elastic network (ElNeDyn), Go-MARTINI, OpenMM/GROMACS protein CG setup, common pitfalls |
references/martini-membranes.md | Lipid library, insane.py membrane builder, CHARMM-GUI CG, protein-membrane embedding, lipid mixing |
references/cgmd-workflows.md | GROMACS CG workflow (mdp parameters, timestep, thermostat), OpenMM CG, backmapping (backward.py), equilibration protocol |
references/cg-analysis.md | MDAnalysis CG trajectories, membrane thickness/APL/order parameters, lateral diffusion, protein CG RMSD/RMSF, density profiles |
"Set up a lipid bilayer simulation" → martini-membranes.md
"Convert my protein to MARTINI CG" → martini-proteins.md
"Run a CG simulation in GROMACS" → cgmd-workflows.md
"Backmap CG structure to all-atom" → cgmd-workflows.md (backward.py section)
"Analyze membrane properties from CG trajectory" → cg-analysis.md
"What resolution should I use?" → cg-theory.md
| Property | Value |
|---|---|
| Mapping ratio | ~4 heavy atoms per bead |
| Timestep (default) | 20 fs (safe: 10–30 fs) |
| Time scaling factor | ×4 (CG time ≈ 4× real time) |
| vdW cutoff | 1.1 nm |
| Electrostatics cutoff | 1.1 nm |
| Recommended thermostat | v-rescale (τ=1 ps) |
| Recommended barostat | Parrinello-Rahman (τ=12 ps) |
| Effective timestep | 80 fs (20 fs × 4 scaling) |
| Accessible timescale | µs per day (GPU) |
homology-modeling or force-fields skillforce-fields skill (OpenMM minimization)mdanalysis skill (most tools work on CG trajectories)~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.