{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/mdcrow-automating-molecular-dynamics","title":"MDCrow: Automating Molecular Dynamics Workflows with Large Language Models","arxiv_id":"2502.09565","date":"2025-02-13","proceeding":null,"authors":["Quintina Campbell","Sam Cox","Jorge Medina","Brittany Watterson","Andrew D. White"],"abstract":"Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate. Recent advances in large language models (LLM) have demonstrated success in automating complex scientific tasks using LLM-based agents. In this paper, we introduce MDCrow, an agentic LLM assistant capable of automating MD workflows. MDCrow uses chain-of-thought over 40 expert-designed tools for handling and processing files, setting up simulations, analyzing the simulation outputs, and retrieving relevant information from literature and databases. We assess MDCrow's performance across 25 tasks of varying required subtasks and difficulty, and we evaluate the agent's robustness to both difficulty and prompt style. \\texttt{gpt-4o} is able to complete complex tasks with low variance, followed closely by \\texttt{llama3-405b}, a compelling open-source model. While prompt style does not influence the best models' performance, it has significant effects on smaller models.","url_abs":"https://arxiv.org/abs/2502.09565v1","url_pdf":"https://arxiv.org/pdf/2502.09565v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"mdcrow-automating-molecular-dynamics","repo_url":"https://github.com/ur-whitelab/MDCrow","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2502.09565","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2502.09565"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/ur-whitelab/MDCrow","reach":null}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"5a0080520de90215","entry":"get_prompt","repo":"ur-whitelab/MDCrow","repo_kind":"official","path":"notebooks/experiments/Robustness/robustness_prompts.py","file_url":"https://github.com/ur-whitelab/MDCrow/blob/HEAD/notebooks/experiments/Robustness/robustness_prompts.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"5a0080520de90215"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}