TABLE 3.

Entropy differences, $T\mathrm{\Delta }{S}_{\text{loop}}^{\text{A}}$ (in kcal/mol) at T=300 K between the free and bound microstates obtained by HSMD for different samples in explicit water^a

Bin size	nf	$T\mathrm{\Delta }{S}_{\text{loop}}^{\text{A}}$			nf	$T\mathrm{\Delta }{S}_{\text{loop}}^{\text{A}}$
		ns = 600	ns = 200	ns = 100		ns = 40
Δαk/30	250	− 1.6	−1.5 (1)	−1.1 (2)	1250	−0.9 (3)
“	500	−1.4	−1.3 (1)	−1.0 (2)	2500	−0.9 (4)
“	750	−1.4	−1.4 (1)	−1.1 (2)	5000	−0.9 (2)
“	1250	−1.3	−1.3 (1)	0.9 (2)	104	−1.0 (2)
Δαk/45	250	−1.6	−1.5 (1)	−1.1 (2)	1250	−0.9 (3)
“	500	−1.4	−1.3 (1)	−1.0 (2)	2500	−0.9 (3)
“	750	−1.4	−1.4 (1)	−1.1 (2)	5000	−0.9 (2)
“	1250	−1.3	−1.3 (1)	0.9 (2)	104	−1.0 (2)

^a $T\mathrm{\Delta }{S}_{\text{loop}}^{\text{A}}$ is defined in eq 24 and its results are given only for the two smallest bins, δ = Δα_k/30 and δ = Δα_k/45, using unit=2.5 ps. The table consists of two parts. The results in the left-hand part are based on 250 ≤ n_f ≤ 1250 and are presented for the entire (two) samples (n_s=600), for the samples’ first 200 conformations, and for n_s=100 by considering every 6th conformation of the entire sample. The results in the right-hand part are based on 1250 ≤ n_f ≤ 10⁴ using samples of n_s=40 by considering every 15th conformation of the entire sample. The statistical error is defined in Table 2; for n_s=600 it is smaller than ±0.1. Results for TΔS^QH and TΔS^LS are not given due to their low accuracy (see Table 2). All calculations were carried out with the AMBER96 force field and 70 TIP3P water molecules.