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  3. Mdcrow: Automating Molecular Dynamics Workflows With Large Language Models.
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  3. Mdcrow: Automating Molecular Dynamics Workflows With Large Language Models.

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MDCrow: automating molecular dynamics workflows with large language models.

Quintina Campbell1, Sam Cox1,2, Jorge Medina1

  • 1Department of Chemical Engineering, University of Rochester, Rochester, NY, United States of America.

Machine Learning: Science and Technology
|April 1, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

MDCrow, an agentic large language model (LLM) assistant, automates molecular dynamics (MD) simulations for proteins. It successfully handles complex tasks, demonstrating the potential of LLM-based agents in scientific research.

Keywords:
agentagentic AIcomputational biologylarge language modelsmolecular dynamics

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Area of Science:

  • Computational Biology
  • Biophysics
  • Artificial Intelligence in Science

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding biomolecular systems.
  • Automating complex MD workflows remains a significant challenge in scientific research.
  • Large language models (LLMs) show promise in automating intricate scientific tasks via agentic approaches.

Purpose of the Study:

  • To introduce MDCrow, an agentic LLM assistant designed to automate protein-focused MD workflows.
  • To evaluate the capabilities of MDCrow in handling diverse and complex MD simulation tasks.
  • To assess the impact of task complexity and prompt style on LLM agent performance.

Main Methods:

  • MDCrow utilizes a chain-of-thought approach, leveraging over 40 specialized tools.
  • Tools cover file management, simulation setup, output analysis, and literature/database retrieval.
  • Performance was evaluated across 25 common MD tasks with varying complexity levels.

    • Main Results:

    • MDCrow demonstrated proficiency in automating a wide range of protein MD simulation tasks.
    • GPT-4o achieved high performance across tasks with minimal variance, followed by Llama3-405b.
    • Prompt style significantly impacted smaller models but not the top-performing LLMs.

    Conclusions:

    • Agentic LLM assistants like MDCrow can effectively automate complex molecular dynamics workflows.
    • Advanced models show robustness in handling complex scientific tasks, indicating a path towards automated scientific discovery.
    • The development of specialized tools enhances the utility of LLMs for specific scientific domains like biophysics.