. Author manuscript; available in PMC: 2019 Mar 19.

Published in final edited form as: J Chem Theory Comput. 2018 Jun 26;14(7):3763–3779. doi: 10.1021/acs.jctc.8b00091

Table 4.

Optimal Values for the Various Harmonic Force Constants in the DNA Model^a

bond type	force constant, k_r(kcal/mol/Å²)	equilibrium value, r₀ (Å)
SP	62.59	3.75
PS	17.63	3.74
SA	44.31	4.85
SG	48.98	4.96
SC	43.25	4.30
ST	46.56	4.40
angle type	force constant, k_α (kcal/mol/rad²)	equilibrium value, α₀ (deg)
PSP	25.67	123.30
SPS	67.50	94.60
PSA	29.53	107.38
PST	39.56	97.18
PSG	26.28	111.01
PSC	35.25	101.49
ASP	67.32	118.94
TSP	93.99	123.59
GSP	62.94	116.90
CSP	77.78	121.43
parameter		value
k_l (Å⁻²)		1.45
k_ϕ (radians⁻²)		3.00
k_d (Å⁻²)		4.00
k_θ (radians⁻²)		1.50
k_ψ (radians⁻²)		0.15

The k_r, k_l, k_ϕ, k_d, k_θ, and k_ψ values correspond to those which are obtained directly from the Boltzmann inversion of distributions obtained from database mining. No further optimization of these parameters was necessary. The angle-specific k_α values correspond to those that reproduce the experimental persistence lengths of ssDNA and were obtained after fine-tuning of the initial parameters obtained from Boltzmann inversion.