# MDClaw

AI agents can now propose atom-level biological hypotheses faster than they can be tested, but trust in an agent-run molecular dynamics simulation rests on a process record, and existing agents leave that record to the language model itself. MDClaw pairs validating tools with a directed acyclic graph (DAG, a graph recording which calculation stages depend on which) that checks stages before execution and records each one; on MDDataBench, which grades against deposited simulations, four open-weight models with MDClaw passed all three runs on 81–100% of 31 test systems. An ablation without the DAG found 11 runs that passed every output check yet had skipped minimization or equilibration, or simulated a different structure.

AI agents can now propose atom-level biological hypotheses faster than they can be tested, but trust in an agent-run molecular dynamics simulation rests on a process record, and existing agents leave that record to the language model itself. MDClaw pairs validating tools with a directed acyclic graph (DAG, a graph recording which calculation stages depend on which) that checks stages before execution and records each one; on MDDataBench, which grades against deposited simulations, four open-weight models with MDClaw passed all three runs on 81–100% of 31 test systems. An ablation without the DAG found 11 runs that passed every output check yet had skipped minimization or equilibration, or simulated a different structure.