Table 2.

HSMD results (in kcal∕mol) for the loop entropy, $T{S}_{\mathrm{loop}}^{\mathrm{A}}$, and for entropy differences $T\Delta S_{\mathrm{loop}}^{\mathrm{A}}$ between the open and closed microstates at T = 300.^a

			$T{S}_{\mathrm{loop}}^{\mathrm{A}}\left(\mathrm{o}\right)$		$T{S}_{\mathrm{loop}}^{\mathrm{A}}\left(\mathrm{c}\right)$		$T\Delta S_{\mathrm{loop}}^{\mathrm{A}}$
Equilbration	bin size, δ	nf	10 ps	16 ps	10 ps	16 ps	10 ps	16 ps
Procedure I	Δαk∕10	10000 (9)	150.9	157.6	147.8	155.4	3.1	2.2
	Δαk∕20	10000 (9)	148.7	151.8	144.8	148.4	3.9	3.4
	Δαk∕40	10000 (9)	148.1	150.4	144.1	146.6	4.0	3.8
	Δαk∕60	500	141.9		138.4		3.5
		1000	143.6		139.3		4.3
		2000 (1)	145.2	155.4	141.0	150.7	4.2	4.7
		4000 (3)	146.6	151.9	142.4	147.4	4.2	4.5
		8000 (7)	147.7	150.2	143.6	146.2	4.1	4.0
		10000 (9)	147.9	150.1	143.8	146.3	4.1	3.8
	Δαk∕80	500	141.9		138.4		3.5
		1000	143.6		139.3		4.3
		2000 (1)	145.2	155.4	140.8	150.6	4.4	4.8
		4000 (3)	146.5	151.8	142.2	147.3	4.3	4.5
		8000 (7)	147.5	150.1	143.4	145.9	4.1	4.2
		10000 (9)	147.7	149.8	143.6	146.0	4.1	3.8
	Δαk∕100	500	141.9		138.5		3.4
		1000	143.6		139.4		4.2
		2000 (1)	145.1	155.4	140.9	150.8	4.2	4.6
		4000 (3)	146.4	151.8	142.1	147.5	4.3	4.3
		8000 (7)	147.2	150.1	143.2	146.0	4.0	4.1
		10000 (9)	147.3	149.7	143.3	145.8	4.0	3.9
Converged							4.0 ± 1.0	3.9 ± 1.0
Procedure II	4.0°	3333					5.3 ± 1.0	5.3 ± 1.0
QH I		8000	198.3	198.3	192.6	192.6		5.7 ± 2.5

^aResults obtained with procedure I based on two equilibration times of 10 and 16 ps for the loop entropy, $S_{\mathrm{loop}}^{\mathrm{A}}$ [Eqs. 13, 14], and the differences, $T\Delta S_{\mathrm{loop}}^{\mathrm{A}}=T[S_{\mathrm{loop}}^{\mathrm{A}}\left(\mathrm{open}\right)-S_{\mathrm{loop}}^{\mathrm{A}}\left(\mathrm{closed}\right)]$ [Eq. 15a]; they were obtained by reconstructing 40 loop structures selected homogeneously from larger MD samples (of 1000 water-loop configurations) of the open and closed microstates. The results are calculated as a function of the bin size δ = Δα_k∕l [Eq. 10] and n_f [Eq. 11], the sample size of the future chains used in the reconstruction process. For the 16 ps results, the n_f values appear in parentheses, e.g., n_f = 8000 (7) means that n_f = 8000 and 7000 for the 10 and 16 ps results, respectively. $S_{\mathrm{loop}}^{\mathrm{A}}$ is defined up to an additive constant that is expected to be the same for both microstates. The maximal statistical error of the results for $T{S}_{\mathrm{loop}}^{\mathrm{A}}$ is 0.7 kcal∕mol. The results for n_f = 10⁴ are bold-faced. For procedure II, the result is presented only for $T\Delta S_{\mathrm{loop}}^{\mathrm{A}}$ with a constant bin size of 4°. $T{S}_{\mathrm{loop}}^{\mathrm{QH}}$ [Eq. 20] is the quasiharmonic entropy; these results were obtained from larger samples of 8000 loop conformations (see text).