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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!

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!

We found that custom built tools are better than just a python REPL, that llama-405B is a great open source model for this, and weaker models require carefully worded instructions. We checked for functionally getting a simulation set up and the correctness of the choices