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.