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NAMD Performance

NAMD 2.8 on ApoA1

92,224 atoms, 12A cutoff + PME every 4 steps, periodic

Time is in seconds per step, averaged over a number of steps, after load balancing. NAMD prints this data, labeled Benchmark time, twice near the beginning of a run. Due to its measurement-based load balancing system, NAMD performance may improve dramatically after the first couple of hundred timesteps.

Download this benchmark: config, directory, 2.8M archive, raw benchmark data

Previous versions: 2.6, 2.5, 2.4, 2.3, 2.2

Independent Performance Analyses

Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood. On the performance of molecular dynamics applications on current high-end systems. Philosophical Transactions: Mathematical, Physical and Engineering Sciences Volume 363, Number 1833, Pages 1987-1998, August 15, 2005. journal

AMBER group MD Benchmarks for Amber, CHARMM and NAMD (updated April, 2005)