Table 2.

Approximate scaling behavior of the CHARMM atom decomposition (AD) model. The table lists the percent parallel efficiency ranges of the AD model for various numbers of processors carrying out MD simulations of proteins in an explicit water environment (50,000–400,000 atoms total) on a) a shared-memory supercomputer (Cray XT4, 2.6 GHz dual-core AMD Opteron nodes) and b) a distributed memory cluster (dual-core 2.8 GHz AMD Opteron nodes, w/8 Gb/s Infiniband interconnects). The simulations were carried out with periodic boundary conditions, PME for long-range electrostatics, an update frequency of 25 steps, an image update frequency of 50 steps, and the BYCB listbuilder. The “COLFFT” columns gives the results with the recently introduced COLFFT code for faster PME calculations on large numbers of CPUs. On the larger systems and for smaller numbers of CPUs (1–4), the default code has faster (2–10%) absolute times (not shown).

a)
	COLFFT	DEFAULT
1	100	100
2	91–95	90–95
4	87–91	78–90
8	82–95	78–83
16	71–79	66–74
32	56–63	50–60
64	39–45	28–38
128	20–28	12–21

b)
	COLFFT	DEFAULT
1	100	100
2	94–99	93–97
4	91–96	88–94
8	86–89	82–86
16	73–80	69–75
32	61–68	56–65
64	17–53	24–47
128	27–40	22–25