The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill retrieves protein structures and metadata from official scientific databases including the Protein Data Bank (files.rcsb.org), AlphaFold (alphafold.ebi.ac.uk), and UniProt (rest.uniprot.org). These operations are standard for the skill's stated purpose and target well-known scientific infrastructure.- [COMMAND_EXECUTION]: The skill executes Python-based simulation workflows. This includes environment dependency checks, system solvation, energy minimization, and production runs. These commands are localized to the simulation environment and do not attempt to interact with sensitive system files or administrative settings.- [SAFE]: All identified operations align with the intended scientific use-case. The code follows best practices for MD simulations, such as checking for steric clashes and potential energy convergence, and provides users with explicit instructions for environment setup rather than performing silent installations.

molecular-dynamics