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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.

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