Table 1.

Parameters used in numerical experiments of protein 2YBB

Parameter	Value	Meaning and Unit
perfil	80	A percentage of the object longest linear dimension to the lattice linear dimension.
grid resolution	0.5–1.0	one grid spacing (Å/grid).
indi	4.0	The internal (molecules) dielectric constant.
exid	80.0	The external (solution) dielectric constant.
prbrad	1.4	A radius (Å) of probe molecule that will define solvent accessible surface in the Lee and Richard’s sense.
salt	0.1	The concentration of first kind of salt,(moles/liter).
bndcon	2	Dipolar boundary condition. The boundary potentials are approximated by the Debye-Huckel potential of the equivalent dipole to the molecular charge distribution.
ionrad	4	The thickness of the ion exclusion layer around molecule (Å).
relpar	0.9	A manually assigned value for relaxation parameter in non-linear iteration convergence process.
maxc	0.0001	The convergence threshold value based on maximum change of potential.
linit	2000	An integer number (> 3) of iterations for solving linear PBE.
ninit	2000	An integer number (>= 0) of iterations for solving non-linear PBE.
energy(s,c,g)	---	Grid, solvation and coulombic energies are calculated.