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seed 9921
timestep 20e-6
steps 600000001
temperature 291
outputPeriod 10000
outputEnergyPeriod 100000
decompPeriod 1000
outputFormat dcd
cutoff 35.0
pairlistDistance 25.0
ParticleDynamicType Langevin
RigidBodyDynamicType Langevin
ParticleLangevinIntegrator BAOAB
## Particles
particle B0
num 65
gridFile null.dx
gridFileScale 1
mass 181.1
transDamping 1240 1240 1240
rigidBodyPotential Bbead
particle B1
num 70
gridFile pmf.dx
gridFileScale 1
mass 181.1
transDamping 1240 1240 1240
rigidBodyPotential Bbead
particle P0
num 65
gridFile null.dx
gridFileScale 1
mass 160.1
transDamping 1240 1240 1240
rigidBodyPotential Pbead
particle P1
num 70
gridFile pmf.dx
gridFileScale 1
mass 160.1
transDamping 1240 1240 1240
rigidBodyPotential Pbead
inputParticles model/dna.coords.txt
systemSize 3000 3000 3000
origin -1500 -1500 -1500
## Interaction potentials
tabulatedPotential 1
tabulatedFile 0@0@model/tabPot/NBBB.dat
tabulatedFile 0@1@model/tabPot/NBBB.dat
tabulatedFile 1@1@model/tabPot/NBBB.dat
tabulatedFile 0@2@model/tabPot/NBPB.dat
tabulatedFile 0@3@model/tabPot/NBPB.dat
tabulatedFile 1@2@model/tabPot/NBPB.dat
tabulatedFile 1@3@model/tabPot/NBPB.dat
tabulatedFile 2@2@model/tabPot/NBPP.dat
tabulatedFile 2@3@model/tabPot/NBPP.dat
tabulatedFile 3@3@model/tabPot/NBPP.dat
tabulatedBondFile model/tabPot/BBP.dat
tabulatedBondFile model/tabPot/BPB.dat
tabulatedBondFile model/tabPot/BPP.dat
tabulatedAngleFile model/tabPot/b1p2b2.dat
tabulatedAngleFile model/tabPot/b1p2p3.dat
tabulatedAngleFile model/tabPot/p1p2b2.dat
tabulatedAngleFile model/tabPot/p1p2p3.dat
tabulatedDihedralFile model/tabPot/b1p1p2b2.dat
tabulatedDihedralFile model/tabPot/b1p2p3b3.dat
tabulatedDihedralFile model/tabPot/p0p1p2p3.dat
inputBonds model/dna.bonds.txt
inputAngles model/dna.angles.txt
inputDihedrals model/dna.dihedrals.txt
inputExcludes model/dna.exculsions.txt
## RigidBodies
rigidBody ssb
num 1
mass 48856.41410648823
inertia 19375322.0 18923208.0 13511100.0
position -1.971286127450211 4.221763283440045 -2.698646477703005
orientation 0.6534513831138611 0.5966775417327881 0.4658081233501434 -0.4628939628601074 -0.17191827297210693 0.8695822358131409 0.5989411473274231 -0.7838494777679443 0.16385820508003235
transDamping 779.075531386 757.10491996 735.261090254
rotDamping 3096.68320292 3027.72621629 3547.0215724
inputRBCoordinates ./model/inputRBCoordinates.txt
potentialGrid Pbead grid-P.dx
potentialGrid Bbead grid-B.dx
potentialGridScale Pbead 0.57827709
potentialGridScale Bbead 0.57827709
gridFile constrain rb_pmf.dx
densityGrid constrain den.dx
pmfScale constrain 1.