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. 2011 Jan 14;134(2):025104. doi: 10.1063/1.3521267

Table 2.

HSMD results (in kcal∕mol) for the loop entropy, TS loop A, and for entropy differences TΔS loop A between the open and closed microstates at T = 300.a

      TS loop A(o)
TS loop A(c)
TΔS loop 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
a

Results obtained with procedure I based on two equilibration times of 10 and 16 ps for the loop entropy, S loop A [Eqs. 13, 14], and the differences, TΔS loop A=T[S loop A( open )S loop A( closed )] [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 = Δαkl [Eq. 10] and nf [Eq. 11], the sample size of the future chains used in the reconstruction process. For the 16 ps results, the nf values appear in parentheses, e.g., nf = 8000 (7) means that nf = 8000 and 7000 for the 10 and 16 ps results, respectively. S loop 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 TS loop A is 0.7 kcal∕mol. The results for nf = 104 are bold-faced. For procedure II, the result is presented only for TΔS loop A with a constant bin size of 4°. TS loop QH [Eq. 20] is the quasiharmonic entropy; these results were obtained from larger samples of 8000 loop conformations (see text).