Table 2. Inferred Potential Parameters Using Contrastive Divergence, for the Protein Models Using the Hard Cutoff and the Lennard-Jones (LJ)-Type van der Waals (vdW) Potentials^a.

vdW and Backbone Stress Potential Parameters
vdW potential	RminCA	RminCB	RminC	RminN	RminO	RminS	ε(RT)	kτ(RT)
hard cutoff	1.57	1.57	1.42	1.29	1.29	2.00		90
LJlearnt	2.43	1.97	1.82	1.74	1.98	3.10	0.018	98
LJCHARMM	2.275	2.175	2.00	1.85	1.70	2.00	b	103
LJAMBER	1.908	1.908	1.908	1.824	1.6612	2.00	c	114

Hydrogen-Bond Potential Parameters
vdW potential	H (RT)	δ (Å)	cos ΘCOH	cos ψOHN
hard cutoff	4.95	2.01	0.770	0.930
LJlearnt	4.98	2.01	0.772	0.928
LJCHARMM	4.80	2.01	0.772	0.925
LJAMBER	4.91	2.01	0.771	0.921

Secondary Structure Bias Potential Parameters
vdW potential	ηβ (RT)	ηα (RT)	Kβ (RT/Å2)	Rβ (Å)
hard cutoff	4.5	18.0	0.80	5.65
LJlearnt	3.7	15.3	0.85	5.39
LJCHARMM	4.5	18.6	1.00	5.62
LJAMBER	2.6	19.7	1.18	5.15

Hydrophobic Interaction Potential Parameters
vdW potential	kh (RT)
hard cutoff	0.030
LJlearnt	0.022
LJCHARMM	0.051
LJAMBER	0.057

^aThe vdW potential parameters of the hard cutoff model were taken from ref (20), while those of the LJ_CHARMM and LJ_AMBER models were taken from the CHARMM⁵⁵ and AMBER⁵⁴ force fields, respectively.

^bε/RT values from the CHARMM force field (0.0338, 0.0929, 0.186, 0.338, 0.203, and 0.760 for the CA, CB, C, N, O, and S atom types respectively).

^cε/RT values from the AMBER force field (0.185, 0.185, 0.145, 0.287, 0.355, and 0.422 for the CA, CB, C, N, O, and S atom types respectively). The potential parameters are described in section 2.3; wherever a unit of length is not indicated, the unit of length is Å.