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# params00-08
# Ion1 - 0.02 M; Ion2 - 0.004 M; Ion Size - 2 A
# Valence1 = 1 e; Valence2 - 1 e
read
mol pqr DNA25.pdb.pqr
end
elec name duplexAsolv
mg-auto
mol 1
ion charge 1 conc 2.0 radius 3.58
ion charge 2 conc 0.000 radius 4.28
ion charge -1 conc 2.0 radius 3.32
cglen 200 200 200
fglen 192 192 192
dime 129 129 129
cgcent mol 1
fgcent mol 1
bcfl mdh
pdie 2.0
sdie 78.54
srfm smol
chgm spl0
srad 1.4
swin 0.3
smpbe vol 7 size 1000
sdens 10
temp 298.15
calcenergy total
calcforce no
write pot dx solvated-DNA-pot
write charge dx DNA-charge
write dielx dx solvated-DNA-dielx
write diely dx solvated-DNA-diely
write dielz dx solvated-DNA-dielz
write kappa dx solvated-DNA-kappa
end
elec name duplexAref
mg-auto
mol 1
ion charge 1 conc 2.0 radius 3.58
ion charge 2 conc 0.000 radius 4.28
ion charge -1 conc 2.0 radius 3.32
cglen 200 200 200
fglen 192 192 192
dime 129 129 129
cgcent mol 1
fgcent mol 1
bcfl mdh
pdie 2.0
sdie 2.0
srfm smol
chgm spl0
srad 1.4
swin 0.3
smpbe vol 7 size 1000
sdens 10
temp 298.15
calcenergy total
calcforce no
write pot dx ref-DNA-pot
write dielx dx ref-DNA-dielx
write diely dx ref-DNA-diely
write dielz dx ref-DNA-dielz
write kappa dx ref-DNA-kappa
end
quit
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