. Author manuscript; available in PMC: 2018 Aug 1.

Published in final edited form as: Biopolymers. 2017 Aug;107(8):10.1002/bip.23020. doi: 10.1002/bip.23020

Table 1.

Atomic Parameters for VDW and Electrostatic Energy and Force Equations.

	well-depth ε (kcal/mol)	radius Rmin/2 (Å)	charge q (e)
Atom
Alkanes
C (1H)	−0.0200	2.2750	0.0
C (2H’s)	−0.0550	2.1750	0.0
C (3,4H’s)	−0.0800	2.0600	0.0
H	−0.0220	1.3200	0.0
TIPS3P
O	−0.1521	1.7682	−0.834
H	−0.0460	0.2245	0.417

The equilibrium well-depth and separations for a pair of atoms are obtained by the following rules: ε_i,j = (ε_i * ε_j)^1/2; Rmin_ij = (Rmin/2)_i + (Rmin/2)_j. The aliphatic carbon atoms are distinguished by the number of hydrogens bound to them.