Looking Under the Streetlight: Evaluation in Generative Molecular Dynamics

This position paper argues that evaluation in generative molecular dynamics (GenMD) exhibits a recurring pattern of comparison against insufficient or misleading benchmarks, which risks over-claiming advantage over classical baselines. The pattern reflects a structural misalignment between common evaluation practices and the scientific tasks the field sets for itself. The reason is structural: the natural ground truth, exhaustive molecular dynamics on the systems of interest, is computationally costly, the very gap that motivates the field. With ground truth inaccessible, evaluation drifts toward convenient proxies, and the resulting norms entrench easily. We identify misaligned evaluation patterns that persist as a community-level equilibrium rather than failures of individual papers, and propose concrete observables, reporting standards, and benchmark designs, both computational and experimental, that better reflect what GenMD aspires to deliver. Our aim is constructive: to give the field shared language and tools for evaluation that match its scientific ambitions before today's conventions calcify into norms.