. Author manuscript; available in PMC: 2018 Sep 12.

Published in final edited form as: J Chem Theory Comput. 2017 Aug 31;13(9):4593–4603. doi: 10.1021/acs.jctc.7b00690

Table 2. Observed values for collective variables parameters.

Quantities are computed for the final 50ns shown in each figure. Percentages are comparison with respect to a single actin monomer, data on the first line of the table (bold). Biased parameters are underlined.

Fig / System + method

〈 d_{24} 〉 (Å)

〈 d_{24}^{2} 〉 (Å^{2})

〈 ϕ_{2134} 〉 (\circ)

〈 ϕ_{2134}^{2} 〉 (\circ^{2})

Fig. 1B/F-actin (1 subunit)

20.62 (0.0%)

425.03 (0.0%)

−6.32 (−0.0%)

40.86 (0.0%)

Fig. 1B/G-monomer

23.82 (15.5%)

568.15 (33.7%)

−16.93 (168.0%)

290.70 (611.4%)

Fig. 1B/F-monomer

26.52 (28.6%)

704.00 (65.6%)

−17.37 (175.0%)

307.00 (651.3%)

Fig. 2B/hENM (no bias)

23.95 (16.2%)

574.24 (35.1%)

−17.44 (176.1%)

317.18 (676.2%)

Fig. 2B/hENM HB K=1000

23.79 (15.4%)

566.72 (33.3%)

−10.54 (66.8%)

116.27 (184.5%)

Fig. 2B/hENM HB K=10000

23.82 (15.5%)

568.04 (33.6%)

−6.95 (9.9%)

49.07 (20.1%)

Fig. 2C/hENM SGD τ^avg = 15 ps

23.88 (15.8%)

570.98 (34.3%)

−6.30 (−0.2%)

54.97 (34.5%)

Fig. 3A/hENM SGD 2 CV

20.62 (−0.0%)

425.72 (0.2%)

−6.48 (2.6%)

52.02 (27.3%)

Fig. 3A/hENM Covar 2 CV

20.65 (0.2%)

427.28 (0.5%)

−6.53 (3.4%)

52.65 (28.8%)

Fig. 3A/hENM SGD 4 CV

20.60 (−0.1%)

425.03 (−0.0%)

−6.50 (2.8%)

50.99 (24.8%)

Fig. 3A&B/hENM Covar 4 CV

20.60 (−0.1%)

424.88 (−0.0%)

−5.99 (−5.2%)

40.03 (−2.0%)

Fig. 3B/hENM LM γ = 0.1

20.62 (0.0%)

425.95 (0.2%)

−6.04 (−4.3%)

44.52 (8.9%)

Fig. 3B/hENM LM γ = 0.01

20.63 (0.0%)

426.02 (0.2%)

−6.07 (−4.0%)

44.63 (9.2%)

Fig. 3B/hENM LM Adapt γ⁰ = 0.1

20.62 (0.0%)

425.94 (0.2%)

−6.02 (−4.7%)

43.97 (7.6%)

Fig. 4A/G-monomer HB 2 CV

20.87 (1.3%)

435.78 (2.5%)

−7.37 (16.7%)

55.38 (35.5%)

Fig. 4A/G-monomer LM Adapt 4 CV

20.55 (−0.3%)

422.51 (−0.6%)

−6.04 (−4.4%)

38.03 (−6.9%)

Fig. 4A/F-monomer LM Adapt 4 CV

20.44 (−0.8%)

418.08 (−1.6%)

−5.11 (−19.1%)

28.01 (−31.5%)

Fig. 4A/F-monomer Fixed Bias 4CV

20.32 (−1.4%)

412.95 (−2.8%)

−4.37 (−30.9%)

20.56 (−49.7%)

Fig. 5/Trimer-A1 LM Adapt

20.32 (−1.4%)

412.90 (−2.9%)

−6.21 (−1.7%)

40.78 (−0.2%)

Fig. 5/Trimer-A2 LM Adapt

20.53 (−0.4%)

421.68 (−0.8%)

−7.03 (11.3%)

51.62 (26.3%)

Fig. 5/Trimer-A3 LM Adapt

20.53 (−0.4%)

421.39 (−0.9%)

−6.75 (6.8%)

47.31 (15.8%)