Biowulf High Performance Computing at the NIH
Acemd v3 benchmarks

June 2020

Benchmarks of Acemd v3 test suite on Biowulf GPU nodes. The test suite is provided with the Acemd package, and is available on Biowulf in /usr/local/apps/acemd/acemd3_examples/.


Details about the simulation conditions are at the Acellera website.

The runs were performed with varying numbers of CPUs. In most cases, 2 CPUs per GPU gave the best performance for a given number of GPUs, therefore all results presented below were done with 2 CPUs per GPU.

Based on these benchmarks, there is a significant performance advantage to the v100 and v100x over the p100 and k80 GPUs. However, in most cases there is no advantage to using more than 1 GPU of any type. Before allocating multiple GPUs for your own Acemd jobs, please run your own benchmarks to verify that the additional GPUs are providing a performance improvement for your jobs. (and please send any interesting results to

DHFR (Dihydrofolate reductase)

Number of atoms: 23,558. Box size: 62.23 Å ✕ 62.23 Å ✕ 62.23 Å

FactorIX (Factor IX)

Number of atoms: 90,906. Box size: 142.09 Å ✕ 83.34 Å ✕ 78.68 Å

STMV (Satellite tobacco mosaic virus)

Number of atoms: 1,067,095. Box size: 221.2 Å ✕ 223.2 Å ✕ 224.5 Å