The Agent Skills Directory

[SAFE]: The skill provides legitimate Python code and instructional content for structural biology and biophysics. All code snippets utilize established, open-source libraries (OpenMM, MDAnalysis, PDBFixer) for their intended scientific purposes.
[EXTERNAL_DOWNLOADS]: The skill recommends installing standard scientific packages from reputable sources like Conda-forge and PyPI. All external links point to official documentation for recognized software tools (e.g., openmm.org, mdanalysis.org, gromacs.org).
[COMMAND_EXECUTION]: Shell commands are restricted to standard package installation (conda install, uv pip install). Python file operations are limited to reading molecular data and writing simulation outputs (logs, trajectories, and plots) to the local workspace, which is standard behavior for this domain.
[DATA_INGESTION]: The skill ingests molecular structure and trajectory files (PDB, DCD, etc.). While these represent external data sources, they are handled by specialized parsers within the scientific libraries, and the skill does not expose any sensitive environment data or perform unauthorized network exfiltration.

molecular-dynamics