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read
mol pqr ion.pqr # Read molecule 1
end
elec name solvated
mg-manual # Use the multigrid method
dime 65 65 65 # Grid dimensions (c 2^(l+1) +1)
# (in x, y, z)
nlev 4 # Number of levels in multilevel
# hierarchy (usually 'l' from above
# definition)
grid 0.33 0.33 0.33 # Grid spacings (A)
# glen 100 100 100 # You can EITHER specify the grid
# lengths OR the grid spacing
gcent mol 1 # This can either be 'mol n' to center
# on a specific molecule or (x, y, z)
# coordinates
chgm spl2 # Charge disc method
mol 1 # Which molecule (1, 2, ...)
lpbe # lpbe/npbe = linear/nonlinear PBE
bcfl mdh # Boundary condition flag
# 0 => Zero
# 1 => Single DH sphere
# 2 => Multiple DH spheres
# 4 => Focusing
ion 1 0.000 2.0 # Counterion declaration:
ion -1 0.000 2.0 # ion <charge> <conc (M)> <radius>
pdie 1.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
chgm spl2 # Charge disc method
srfm smol # Surface calculation method
# 0 => Mol surface for epsilon;
# inflated VdW for kappa; no
# smoothing
# 1 => As 0 with harmoic average
# smoothing
# 2 => Cubic spline
sdens 10.0
srad 1.4 # Solvent radius
swin 0.3 # Surface cubic spline window
temp 298.15 # Temperature
gamma 0.105 # Surface tension (in kJ/mol/A^2)
calcenergy total # Energy I/O (to stdout)
# 0 => don't write out energy
# 1 => write out total energy
# 2 => write out total energy and all
# components
calcforce no # Atomic forces I/O (to stdout)
# 0 => don't write out forces
# 1 => write out net forces on molecule
# 2 => write out atom-level forces
end
elec name reference
mg-manual # Use the multigrid method
dime 65 65 65 # Grid dimensions (c 2^(l+1) +1)
# (in x, y, z)
nlev 4 # Number of levels in multilevel
# hierarchy (usually 'l' from above
# definition)
grid 0.33 0.33 0.33 # Grid spacings (A)
# glen 100 100 100 # You can EITHER specify the grid
# lengths OR the grid spacing
gcent mol 1 # This can either be 'mol n' to center
# on a specific molecule or (x, y, z)
# coordinates
mol 1 # Which molecule (1, 2, ...)
lpbe # lpbe/npbe = linear/nonlinear PBE
bcfl mdh # Boundary condition flag
# 0 => Zero
# 1 => Single DH sphere
# 2 => Multiple DH spheres
# 4 => Focusing
ion 1 0.000 2.0 # Counterion declaration:
ion -1 0.000 2.0 # ion <charge> <conc (M)> <radius>
pdie 1.0 # Solute dielectric
sdie 1.0 # Solvent dielectric
chgm spl2 # Charge disc method
sdens 10.0
srfm smol # Surface calculation method
# 0 => Mol surface for epsilon;
# inflated VdW for kappa; no
# smoothing
# 1 => As 0 with harmoic average
# smoothing
# 2 => Cubic spline
srad 1.4 # Solvent radius
swin 0.3 # Surface cubic spline window
temp 298.15 # Temperature
gamma 0.105 # Surface tension (in kJ/mol/A^2)
calcenergy total # Energy I/O (to stdout)
# 0 => don't write out energy
# 1 => write out total energy
# 2 => write out total energy and all
# components
calcforce no # Atomic forces I/O (to stdout)
# 0 => don't write out forces
# 1 => write out net forces on molecule
# 2 => write out atom-level forces
end
print energy 1 - 2 end
quit
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