Molecular dynamics (MD) simulations are among the most demanding workloads in computational science. Using them, researchers can observe atomic behavior in extraordinary detail, from protein folding to drug and materials discovery.

But they come at a steep cost. Simulations model hundreds of thousands to tens of millions of atoms, advancing femtoseconds per step across billions of steps. Because problem size is typically fixed, parallelization must spread work across all available resources simultaneously, a regime known as strong scaling.

GROMACS is one of the world’s most widely used MD packages. Modern hardware and heterogeneous CPU-GPU parallelization has pushed performance into the sub-millisecond regime, reaching 100–200 microseconds per time-step across multiple GPUs.…