MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

MDForge is an LLM-based agent designed to automate the pipeline design for molecular dynamics simulations, utilizing a novel approach that incorporates online verbal rewards and multi-agent debate among physics experts. It has shown competitive performance against human experts on three SAMPL host-guest binding free-energy benchmarks, successfully discovering a high-affinity binder for CB[7] confirmed by NMR. This advancement is significant for practitioners as it streamlines the pipeline design process, reducing the need for extensive expert knowledge and trial-and-error in molecular simulations.