A Multi-Agent Framework for Automated Coarse-Grained Molecular Dynamics of Polymers

Computer Science > Artificial Intelligence [Submitted on 7 Aug 2026] A Multi-Agent Framework for Automated Coarse-Grained Molecular Dynamics of Polymers Joohee Choi, Junhyeong Lee, Seunghwa Ryu Coarse-grained (CG) molecular dynamics extends polymer simulation beyond the scales accessible to all-atom (AA) methods, but bottom-up CG modeling is laborious. The CG resolution is a design choice, so a transferable parameter set is generally not available and the potentials are derived anew for each polymer mapping. Here we present CGMas, a multi-agent framework that automates topology construction, equilibration, mapping, potential derivation, and validation from a natural-language specification of the polymer and target resolution. A large-language-model (LLM) reasoning agent infers the AA topology from polymer name, while layered self-correction resolves physical errors common to unsaturated, heteroatom-containing, and polar polymers. Downstream agents equilibrate the system, map it onto CG representation, derive potentials through Boltzmann inversion, and benchmark the model against its atomistic reference. CGMas completed all 27 homopolymer and copolymer tasks, matched the AA density to within 5% in 22, and reduced simulation from 38-88 min to 1 min, establishing agentic LLMs as a route to automated polymer coarse-graining. Subjects: Artificial Intelligence (cs.AI); Multiagent Systems (cs.MA) Cite as: arXiv:2608.06694 [cs.AI]   (or arXiv:2608.06694v1 [cs.AI] for this version)   https://doi.org/10.48550/arXiv.2608.06694 Focus to learn more Submission history From: Junhyeong Lee [view email] [v1] Fri, 7 Aug 2026 01:47:48 UTC (27,311 KB) Access Paper: HTML (experimental) view license Current browse context: cs.AI < prev   |   next > new | recent | 2026-08 Change to browse by: cs cs.MA References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)