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. 2004 Jan;86(1):50–57. doi: 10.1016/S0006-3495(04)74082-5

TABLE 2.

Hopping rates estimated from the simulations

krkl (#/ns) kr + kl (#/ns) kl (#/ns) kr (#/ns) kr/kl Inline graphic
sim1 −3.9 ± 0.3 5.7 ± 1.4 4.8 ± 0.7 0.9 ± 0.7 0.19 0.27
sim2 −1.9 ± 0.6 5.1 ± 1.4 3.5 ± 0.8 1.6 ± 0.8 0.46 0.52
sim3 2.0 ± 0.3 4.0 ± 0.4 1.0 ± 0.3 3.0 ± 0.3 3.1 1.9
sim4 2.3 ± 0.3 4.6 ± 0.4 1.1 ± 0.2 3.5 ± 0.2 3.1 3.7

For each channel, the trajectory of the collective coordinate X for water molecules in the defined region (length L = 15 Å) was obtained as described in the text. krkl was calculated from the total displacement of X in 4 ns, according to Eq. 19. To calculate kr + kl, the 4-ns trajectory of X was divided into 20 subtrajectories, each of 200 ps duration. For each t, the variance of the displacements in the 20 subtrajectories during time t was computed, and kr + kl was calculated from the slope of the variance-t curve, according to Eq. 20. kr, kl, and kr/kl were obtained from krkl and kr + kl. The last column (Inline graphic* of the table is the predicted value of kr/kl, calculated from exp(−Δμ/kBT) (Eq. 6), using T = 310 K and Δμ taken from Table 1.