We introduce ColPackAgent, an agent framework that autonomously runs Monte Carlo simulations of colloidal packing through a Model Context Protocol (MCP) tool server and an agent skill, whether as a standalone agent or inside an existing agent system. By harnessing the MCP server and agent skill, ColPackAgent executes a structured workflow for colloidal packing simulations, which are central to studies of phase behavior, self-assembly, and materials design. Without dedicated simulation tools and workflow instructions, general-purpose Large Language Model (LLM) agents tend to describe such workflows rather than execute them reliably. The MCP server exposes a custom-built colpack Python package that wraps HOOMD-blue hard-particle Monte Carlo, and the skill encodes a four-stage workflow contract. ColPackAgent can carry out the workflow interactively with human feedback, autonomously from an end-to-end prompt, or as autoresearch following a provided program file. We demonstrate the system in different modes with several colloidal packing simulation examples such as cube particles in 3D, a binary system of disks and capsules in 2D, and the 2D hard-disk freezing transition using autoresearch. We also compare model performance on this workflow across a panel of LLMs with 17 stage-specific prompts. This benchmark provides a stage-level check of how reliably different models follow the setup, planning, and analysis workflow. Together, these results show that pairing a domain Python package with MCP tools and a portable agent skill provides a practical route for turning a simulation toolkit into an agent-assisted research workflow.
The promise of AI-driven scientific discovery hinges on whether AI agents can autonomously design and execute the computational workflows that underpin modern science. Molecular dynamics (MD) simulation presents a natural test bed to stress-test this claim; it requires translating physical intuition into syntactically and semantically correct input scripts, reasoning about initial and boundary conditions, diagnosing numerically unstable trajectories, and interpreting outputs against known physical behavior and laws. We introduce MDGYM, a benchmark of 169 expert-curated MD simulations spanning LAMMPS and GROMACS, two widely used MD packages, across three increasing difficulty levels. We evaluate three agentic frameworks -- Claude Code, Codex, and OpenHands -- with four LLMs, and find that all perform poorly: even the strongest agent solves only 21% of easy-level tasks, with less than 10% at higher difficulties. Trajectory analysis reveals a characteristic pattern of failure -- agents successfully invoke simulation machinery but produce physically unstable configurations, fabricate numerical outputs without executing the underlying computation, or abandon tasks prematurely rather than iterating through simulation-specific errors. These failure modes are qualitatively distinct from those observed in general software engineering benchmarks, indicating that fluent code generation does not transfer to grounded physical reasoning.
Long-running molecular simulation campaigns require repeated continuation from saved states, provenance-aware progression, adaptive assessment, and occasional interpretation of workflow conditions that cannot be resolved safely by fixed rules. Here, we present Agent-MD, a framework that places large language model (LLM) reasoning selectively at campaign construction and event-triggered review, while routine simulation, analysis, continuation, archiving, and state progression are handled by a persistent rule-based campaign agent using approved policies and explicit state records. Agent-MD was demonstrated in a grand canonical Monte Carlo-molecular dynamics (GCMC-MD) water-vapor desorption campaign comprising five montmorillonite systems and three sequential relative-humidity states (RH = 0.9-0.3-0.1). Across 15 system-RH states, the workflow completed 120 segmented simulation cycles with state-specific sampling lengths and provenance-aware restart inheritance. Routine production required no live reasoning-agent invocation, while one state reached a review boundary; two preserved incidents were subsequently evaluated through blinded reasoning-agent replay, which identified the underlying workflow problems and recommended appropriate follow-up actions. The simulations also revealed distinct composition-dependent low-RH responses, with Ca-bearing montmorillonite retaining more interlayer water and maintaining a larger basal spacing than the Na- and K-bearing systems, while the highest-charge Na system retained more residual water under dry conditions. These results demonstrate that long-running scientific workflows need not place every operation inside an LLM reasoning loop: selective reasoning can instead be combined with deterministic execution, structured evidence, and validated control handoffs to provide reproducible and auditable agent-assisted molecular simulation.
The Model Context Protocol (MCP) has unified the interface between Large Language Models (LLMs) and external tools, yet a fundamental gap remains in how agents conceptualize the environments within which they operate. Current paradigms are bifurcated: Task-level planning often ignores execution-time dynamics, while reactive execution lacks long-horizon foresight. We present MCP-Cosmos, a framework that infuses generative World Models (WM) into the MCP ecosystem to enable predictive task automation. By unifying three disparate technologies, namely MCP, World Model, and Agent, we demonstrate that a "Bring Your Own World Model" (BYOWM) strategy allows agents to simulate state transitions and refine plans in a latent space before execution. We conducted experiments using two strategies, namely ReAct and SPIRAL with 2 planning models and 3 representative world models over 20+ MCP-Bench tasks. We observed improvements in Agent's environment interaction KPI such as tool success rate and tool parameter accuracy. The framework also offers new metrics such as Execution Quality to generate new insights about the effectiveness of world models compared to baseline.