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Molecular dynamics requires a lot of expert knowledge to set-up and analyze simulations. We set out to automate it with LLM agents: MDCrow!

Work by Quintina Campbell, Sam Cox, Jorge Medina, Brittany Watterson. They wanted to see if agents could handle complex multi-step tasks like fetching a protein input structure, running the simulation and analysis. They built several tasks with varying complexity.

Models do pretty well on the tasks – with GPT-4o getting 72% and Llama-3.1 405B getting 68%. Some models, like Claude Sonnet, would do better but just couldn’t figure out NPT ensembles!