aiqbench analysis
PolyJarvis represents a significant step toward automating complex molecular dynamics workflows by using an LLM planning agent to orchestrate deterministic scripts for simulating amorphous polymers. The system successfully predicts key material properties like density and glass transition temperature for seven homopolymers, though it shows specific limitations with certain force fields in predicting stiffness and density. This approach lowers the barrier to entry for high-fidelity materials simulation by replacing manual expertise with a validated, agent-driven pipeline.
PolyJarvis: An LLM-Orchestrated Agent for Automated All-Atom Molecular Dynamics of Amorphous Homopolymers
arXiv:2604.02537v3 Announce Type: replace Abstract: All-atom molecular dynamics (MD) simulations can predict polymer properties from molecular structure, yet their execution requires specialized expertise in force field selection, system construction, equilibration, and property extraction. We present PolyJarvis, a platform in which a planning agent produces a validated run plan that deterministic stage scripts execute through established simulation toolkits, Enhanced Monte Carlo (EMC) for system construction and LAMMPS for molecular dynamics, exposed as Model Context Protocol (MCP) servers, with a recovery agent consulted only on structured failures and within a fixed decision budget. Given a repeat-unit SMILES string and target properties, PolyJarvis constructs the amorphous cell, equilibrates it under a mechanized convergence gate, and computes target properties. Validation is conducted on seven amorphous homopolymers, each run as three replicates that share a protocol frozen per system and use independent random seeds, namely polyethylene (PE), atactic polystyrene (aPS), syndiotactic poly(vinyl chloride) (sPVC), poly(L-lactic acid) (PLLA), poly(ethylene glycol) (PEG), poly(ether ether ketone) (PEEK), and polysulfone (PSU). Against experimental references, 13 of 19 graded comparisons meet the acceptance criteria (density 5 of 7, glass transition 4 of 7, bulk modulus 4 of 5). The failures are concentrated in the PCFF systems: under-density of aPS and PEG, overestimated glass transitions of the stiff PLLA and PEEK backbones, and an overstiff PEG bulk modulus.
Abstract:All-atom molecular dynamics (MD) simulations can predict polymer properties from molecular structure, yet their execution requires specialized expertise in force field selection, system construction, equilibration, and property extraction. We present PolyJarvis, a platform in which a planning agent produces a validated run plan that deterministic stage scripts execute through established simulation toolkits, Enhanced Monte Carlo (EMC) for system construction and LAMMPS for molecular dynamics, exposed as Model Context Protocol (MCP) servers, with a recovery agent consulted only on structured failures and within a fixed decision budget. Given a repeat-unit SMILES string and target properties, PolyJarvis constructs the amorphous cell, equilibrates it under a mechanized convergence gate, and computes target properties. Validation is conducted on seven amorphous homopolymers, each run as three replicates that share a protocol frozen per system and use independent random seeds, namely polyethylene (PE), atactic polystyrene (aPS), syndiotactic poly(vinyl chloride) (sPVC), poly(L-lactic acid) (PLLA), poly(ethylene glycol) (PEG), poly(ether ether ketone) (PEEK), and polysulfone (PSU). Against experimental references, 13 of 19 graded comparisons meet the acceptance criteria (density 5 of 7, glass transition 4 of 7, bulk modulus 4 of 5). The failures are concentrated in the PCFF systems: under-density of aPS and PEG, overestimated glass transitions of the stiff PLLA and PEEK backbones, and an overstiff PEG bulk modulus.
Computation and Language (cs.CL); Materials Science (cond-mat.mtrl-sci)
arXiv:2604.02537 [cs.CL]
(or arXiv:2604.02537v3 [cs.CL] for this version)
https://doi.org/10.48550/arXiv.2604.02537 Focus to learn more arXiv-issued DOI via DataCite
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Full text under the publisher's open licence · 308 words
