An auditable harness for biomolecular dynamics simulations by AI agents
Year: 2026
Type: preprint
Abstract: AI agents now generate biological hypotheses faster than they can be tested. Hypotheses stated at the atomic level can be examined with molecular dynamics (MD) simulations. For new questions without a reference, trust in an agent-run simulation rests on a tool-written process record, not the agent's account. Existing MD agents leave this record to the language model. Here we present MDClaw, a harness whose validating tools and directed acyclic graph (DAG) check stages before execution and record every simulation stage. On MDDataBench, which grades outputs against deposited simulations, four open-weight models with MDClaw passed all three runs on 81-100% of 31 test systems. The DAG complements this outcome check. An ablation without the DAG revealed 11 successful runs that had skipped minimization or equilibration, or simulated a different structure. MDClaw carried questions from human and AI scientists through simulation to trajectories traceable to their inputs and settings.
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: green
OpenAlex ID: W7225773237
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