Table 5. Timings for MDGX or PMEMD on a single processor.

20000 steps of dynamics were run using PMEMD or MDGX in SPME or MLE mode on an Intel Q9550 processor (Core2 architecture, 6MB L2 cache, 2.83GHz clock speed). Simulations made use of the parameters in Table 6; the PMEMD simulation for the “aggressive” parameters used I^(pm) = 4 and g = 32. Timings for different categories of calculations in the MDGX code were measured using the UNIX gettimeofday() function; those in the PMEMD code were measured with PMEMD’s internal profiling functions. Because the two programs are structured differently, the exact content of each category of calculation may not match exactly—for instance, MDGX and PMEMD use different styles of pair list, and the convolution kernel is computed more rapidly in MDGX than PMEMD because PMEMD always computes virial contributions while MDGX skips them if they are not needed. Total run times for both programs are greater than the sums of all categories in each column because timings for miscellaneous routines are not listed. Standard deviations were collected over ten trials to estimate errors in the timings; they were less than 1% across all categories, but are omitted to condense the table.

Routine	Conservative		Aggressive
	SPME	MLE	PMEMD	SPME	MLE
Bonded Interactions	5.8	5.9	4.6	5.8	5.8
ΔE(dir), Pair List	7.7	7.9	31.3	7.7	7.8
ΔE(dir), Interactions	383.9	383.6	216.7	323.8	323.9
ΔE(dir), Total	391.6	391.6	248.0	331.5	331.7
ΔE(rec), B-Splines	14.3	14.4	2.6	14.2	14.3
ΔE(rec), Particle → Mesh	16.2	16.4	6.0	15.9	16.1
ΔE(rec), Convolution a	2.4	1.2	11.6	1.7	0.8
ΔE(rec), FFT	17.3	22.6	28.4	9.1	11.8
ΔE(rec), Mesh → Particle	22.5	22.6	11.1	22.2	22.3
Mesh ⇋ Mesh b		42.1			29.0
ΔE(rec), Total	72.8	119.3	59.8	63.1	94.2
Total Wall Time	473.1	522.5	316.1	405.9	435.6

^aMultiplication of the charge mesh and reciprocal space pair potential in Fourier space

^bInterpolation between different levels of MLE mesh