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.