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.
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)