Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principles physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent’s behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host–guest binding free-energy benchmarks (CB[7], OAH, CBClip), MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder (K_a ≈ 8 × 10¹² M^-1). Our data and code are available at https://github.com/Zehong-Wang/MDForge.

Multi-agent systems built from large language models are deployed widely, yet how much performance is lost when two LLMs must coordinate rather than act alone remains unclear. We formulate the collaboration tax as the team-decentralisation loss of a two-player cooperative game with private information, with two propositions characterising its sign and its equivalence to a max-superadditivity violation. We operationalise this definition on 32 solo-tractable tasks grouped by source of grounding friction and measure it on 11 models from 7 providers. The tax is structured along two no-exception axes: a category ordering across every model and a monotonic decrease with capability. The proximate mechanism is not a reasoning deficit but a four-stage conversational cascade in which agents make ungrounded claims, fail to query the partner, skip integrating both views, and accept the answer without re-derivation. The tax is mechanically predictable from conversation features and partly tractable: a prompt intervention targeting all four stages closes a substantial fraction of the gap, with the dominant bottleneck differing across categories. In heterogeneous pairs the tax is pulled toward the stronger partner rather than the additive midpoint, empirically realising the max-superadditivity violation predicted by our framework. Together these results recast collaboration in LLM systems as a measurable, predictable, and partly tractable cost.