Automating MD simulations for Proteins using Large language Models: NAMD-Agent
This work introduces an automated pipeline using a Large Language Model (LLM) to create and run Molecular Dynamics (MD) simulations with minimal human input. The system uses agentic AI to interpret natural language prompts, automatically build protein systems using CHARMM-GUI, execute NAMD simulations, and perform structural analyses like RMSD. It successfully generated valid simulation setups for various systems.