#############################################################################
### BORN ION SOLVATION ENERGY
### $Id: apbs-mol-auto.in 1119 2007-07-23 13:52:03Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for 
### input file sytax.
#############################################################################

# READ IN MOLECULES
read                                                
    mol pqr born-ion.pqr
end

# COMPUTE POTENTIAL FOR SOLVATED STATE
elec name solvated
    mg-auto      
    dime 65 65 65
    cglen 50 50 50
    fglen 12 12 12
    fgcent mol 1
    cgcent mol 1
    mol 1
    lpbe
    bcfl mdh
    pdie 1.0
    sdie 78.54
    chgm spl0
    srfm spl2
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx solvated-born-pot
    write charge dx born-charge
    write dielx dx solvated-born-dielx
    write diely dx solvated-born-diely
    write dielz dx solvated-born-dielz
    write kappa dx solvated-born-kappa
end

# COMPUTE POTENTIAL FOR REFERENCE STATE
elec name reference
    mg-auto
    dime 65 65 65
    cglen 50 50 50
    fglen 12 12 12
    fgcent mol 1
    cgcent mol 1
    mol 1
    lpbe
    bcfl mdh
    pdie 1.0
    sdie 1.0
    chgm spl0
    srfm spl2
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx ref-born-pot
    write dielx dx ref-born-dielx
    write diely dx ref-born-diely
    write dielz dx ref-born-dielz
    write kappa dx ref-born-kappa
end

# COMBINE TO GIVE SOLVATION ENERGY
print elecEnergy solvated - reference end
print elecEnergy solvated end
print elecEnergy reference end

quit
