Table 1.

Speed of computation: explicit vs. implicit solvent

Simulation method	Structure and conformational change
	Protein χ1, χ2 flips	Nucleosome tail collapse	Nucleosome DNA unwrap	Miniprotein folding
Explicit solvent TIP3P PME	20.55 ± 0.02	1.79 ± 0.02	0.92 ± 0.02	74 ± 1
GB (nominal speed)	21.86 ± 0.26	1.13 ± 0.00	1.39 ± 0.006	574 ± 2
GB (effective speed)	32.79 ± 0.40	1.4 ± 0.6/8 ± 3/113 ± 68	42 ± 28	4018 ± 1768

Nominal speed is the number of nanoseconds of simulation time per day of wall clock time (ns/day). Effective speed = (nominal speed) × (conformational sampling speedup). Qualitatively, the effective speed is the estimated simulation time required by the explicit-solvent TIP3P PME simulation to sample conformational space comparable to the corresponding GB simulation run for 1 day on the same resource. The three time values for the nucleosome tail collapse represent the results for the collapse of the H3, H2B′, and H3′ tails, respectively. Langevin collision frequency is γ = 0.01 ps⁻¹; AMBER-12 on a single GTX680 GPU card with the SPFP precision model.