MDArena introduces 50 containerized tasks drawn from active biomolecular simulation projects, covering 29 molecular systems and 14 research protocols, including trajectory analysis, system preparation, free-energy calculations, and enhanced sampling. Across six Codex and OpenCode configurations, Codex GPT-5.5 with extra-high reasoning achieves the best Strict-Pass@1 result at 24/50, or 48%. Higher correctness and process rewards than strict success rates suggest useful partial progress, but agents still fail on details required for reproducible workflows. Membrane-protein preparation and alchemical free-energy setup remain especially difficult.
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