Table 5.

HSMD results (in kcal/mol) for the entropy, $T{S}_{\text{loop}}^{\mathrm{A}}$ (equation (46)) and $T\Delta S_{\text{loop}}^{\mathrm{A}}$ at T=300 K for the free and bound microstates of the loop of α-amylase in explicit water^a

		Free loop	Bound loop
Bin size	nf (j)	$T{S}_{\text{loop}}^{\mathrm{A}}$	$T{S}_{\text{loop}}^{\mathrm{A}}$	$T\Delta S_{\text{loop}}^{\mathrm{A}}$
Δαk/15	250 (1)	67.18 (4)	68.72 (4)	−1.5
“	500 (2)	66.48 (7)	67.86 (8)	−1.4
“	750 (3)	66.17 (4)	67.58 (8)	−1.4
“	1250 (5)	65.74 (4)	67.19 (8)	− 1.4
Δαk/30	250 (1)	67.04 (9)	68.61 (7)	−1.6
“	500 (2)	66.22 (7)	67.61 (7)	−1.4
“	750 (3)	65.77 (4)	67.15 (8)	−1.4
“	1250 (5)	65.19 (4)	66.49 (3)	− 1.3
Δαk/45	250 (1)	67.03 (4)	68.60 (5)	−1.6
“	500 (2)	66.17 (7)	67.56 (7)	−1.4
“	750 (3)	65.69 (4)	67.08 (8)	−1.4
“	1250 (5)	65.06 (4)	66.36 (8)	− 1.3
TS QH		78.6 (1)	87 (6)	−.8 (7)
TS LS		87.4 (1)	90 (7)	−2.6 (8)

^aThe results are taken from Cheluvaraja et al., 2008. The bin sizes are δ=Δα_k/l(equation (44)). n_f denotes the sample size of the future chains used in the reconstruction process, n_f = unit×j, where j is the number of simulations of unit size applied at each reconstruction step. Generation of the samples (of 600 conformations) and their reconstruction is based on the AMBER force field and 70 TIP3P water molecules. The statistical error in defined in Table 1; for $T\Delta S_{\text{loop}}^{\mathrm{A}}$ the errors are smaller than ±0.1. S^QH (equation (4)) is the quasi-harmonic entropy and S^LS is $\Delta S_{\text{loop}}^{\mathrm{A}}$ obtained by the local states method using b=2 and the discretization parameter, l=10 (see Appendix). These results that were obtained from larger samples are strongly inaccurate. The entropy $T{S}_{\text{loop}}^{\mathrm{A}}$ is defined up to an additive constant that is expected to be the same for both microstates. As anticipated, the results for $T{S}_{\text{loop}}^{\mathrm{A}}$ decrease systematicallyas the approximation improves (i.e., as δ is decreased and n_f is increased). The results for $T\Delta S_{\text{loop}}^{\mathrm{A}}$ are stable converging to 1.3±0.2 kcal/mol.