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