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This is a documentation-only Amber molecular dynamics guide with expected local command examples and no hidden execution or credential access.
Install this if you want a manual Amber MD workflow reference. Run commands deliberately in a project directory, verify Amber/AmberTools installation sources, and expect local compute and storage use; the artifacts do not show hidden execution, secret handling, or data exfiltration.
---
name: amber-md
description: |
Official-style Amber24 molecular dynamics workflow guide for proteins. Includes a standard end-to-end Amber MD procedure, command templates, input-file templates, and a complete manual worked example from PDB download through RMSD/RMSF analysis. This is a documentation-oriented scientific skill for reproducible research workflows in Amber.
metadata:
{
"openclaw":| 4. NVT heating | raise temperature to target value | heated restart + trajectory | | 5. NPT equilibration | stabilize density and pressure | equilibrated restart + trajectory | | 6. Production MD | generate scientific trajectory | production trajectory | | 7. Analysis | compute RMSD/RMSF and related metrics | data tables and plots | ---
### Recommended analysis procedure Before RMSD/RMSF: - strip solvent and ions if you want protein-only metrics, - apply `autoimage`, - use a consistent atom mask.
### Step 7 — inspect results ```bash ls -lh md/prod.nc analysis/rmsd_ca.dat analysis/rmsf_ca.dat ``` Expected scientific interpretation:
65/65 vendors flagged this skill as clean.