molecular-dynamics
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
SkillSpector found no issues but could not fully inspect the package, usually because SKILL.md refers to a file that is not present, so it fails closed to CAUTION instead of SAFE. Read it as "not fully checked", not as a finding. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
- Package
- 3 files, 32 KB
- SKILL.md
- 1832 words, 12+ sections
- Code
- None. Instructions only.
- License
- MIT
- Compatibility
- Requires Python 3.11+ with OpenMM and MDAnalysis; matplotlib for plots. Optional PDBFixer and OpenFF need separate installation. Network access for installation; local simulation and analysis run offline.
SKILL.md covers: Molecular Dynamics · Overview · Windows: use .venv-md/Scripts/python.exe instead · When to Use This Skill · Core Workflow: OpenMM Simulation · 1. System Preparation · 2. Energy Minimization · 3. NVT Equilibration · 4. NPT Equilibration and Production · Trajectory Analysis with MDAnalysis · 1. Load Trajectory · 2. RMSD Analysis
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 19 KB |
references/mdanalysis_analysis.md | doc | 9.2 KB |
references/system_preparation.md | doc | 4.8 KB |
External hosts referenced
docs.mdanalysis.org docs.openmm.org docs.openforcefield.org github.com openmm.org ambermd.org charmm-gui.org manual.gromacs.org mdanalysis.org www.ks.uiuc.edu
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-molecular-dynamics-scan.json
- Badge for your README:
- Request a re-scan