seed 289712415 timestep 2e-05 steps 10000000000 numberFluct 0 # deprecated rigidBodyGridGridPeriod 20 interparticleForce 1 # other values deprecated fullLongRange 0 # deprecated temperature 291 outputPeriod 10000 ## Energy doesn't actually get printed! outputEnergyPeriod 10000 outputFormat dcd ## Infrequent domain decomposition because this kernel is still very slow decompPeriod 10000 cutoff 35 pairlistDistance 25 origin -500.0 -500.0 -500.0 systemSize 1000 1000 1000 ParticleDynamicType Langevin RigidBodyDynamicType Langevin ParticleLangevinIntegrator BAOAB particle B num 70 mass 181.1 transDamping 1240 1240 1240 diffusion 43.5 gridFile potentials/plane.dx gridFileScale 1. rigidBodyPotential Bbead1 rigidBodyPotential Bbead2 particle B2 num 36 diffusion 43.5 mass 181.1 transDamping 1240 1240 1240 gridFile potentials/plane.dx gridFileScale 1. rigidBodyPotential B2bead1 rigidBodyPotential B2bead2 particle P num 70 diffusion 43.5 mass 160.1 transDamping 1240 1240 1240 gridFile potentials/plane.dx gridFileScale 1. rigidBodyPotential Pbead1 rigidBodyPotential Pbead2 particle P2 num 36 diffusion 43.5 mass 160.1 transDamping 1240 1240 1240 gridFile potentials/plane.dx gridFileScale 1. rigidBodyPotential P2bead1 rigidBodyPotential P2bead2 inputRestraints restraint.txt ## Input coordinates restartCoordinates dsdna18-ssdna70.0.restart restartMomentum dsdna18-ssdna70.0.momentum.restart ## Interaction potentials tabulatedPotential 1 ## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file tabulatedFile 0@0@potentials/example-nb.B-B.dat tabulatedFile 0@1@potentials/example-nb.B-B2.dat tabulatedFile 0@2@potentials/example-nb.B-P.dat tabulatedFile 0@3@potentials/example-nb.B-P2.dat tabulatedFile 1@1@potentials/example-nb.B2-B2.dat tabulatedFile 1@2@potentials/example-nb.B2-P.dat tabulatedFile 1@3@potentials/example-nb.B2-P2.dat tabulatedFile 2@2@potentials/example-nb.P-P.dat tabulatedFile 2@3@potentials/example-nb.P-P2.dat tabulatedFile 3@3@potentials/example-nb.P2-P2.dat tabulatedBondFile tabPot/BPB.dat tabulatedBondFile potentials/bond-1.000-8.410.dat tabulatedBondFile potentials/bond-1.000-7.960.dat tabulatedBondFile tabPot/BPP.dat tabulatedBondFile tabPot/BBP.dat tabulatedBondFile potentials/bond-10.000-7.835.dat tabulatedAngleFile tabPot/p1p2b2.dat tabulatedAngleFile potentials/angle-90.000-87.000.dat tabulatedAngleFile potentials/angle-90.000-150.000.dat tabulatedAngleFile potentials/angle-90.000-162.000.dat tabulatedAngleFile tabPot/b1p2b2.dat tabulatedAngleFile tabPot/b1p2p3.dat tabulatedAngleFile tabPot/p1p2p3.dat tabulatedDihedralFile tabPot/b1p2p3b3.dat tabulatedDihedralFile tabPot/b1p1p2b2.dat tabulatedDihedralFile tabPot/p0p1p2p3.dat inputBonds potentials/example.bonds.txt inputAngles potentials/example.angles.txt inputDihedrals potentials/example.dihedrals.txt inputExcludes potentials/example.exculsions.txt rigidBody ssb1 num 1 mass 48856.4140625 inertia 19375326.0 18923212.0 13511158.0 inputRBCoordinates inputSSBCoords.txt transDamping 779.396325558 757.577520666 735.633430273 rotDamping 3097.88531206 3029.1232551 3548.84746686 gridFile constrain potentials/plane.dx densityGrid constrain den.dx pmfScale constrain 1. potentialGrid Pbead1 grid-P.dx potentialGrid Bbead1 grid-B.dx potentialGridScale Pbead1 0.5782764 potentialGridScale Bbead1 0.5782764 potentialGrid P2bead1 grid-P2.dx potentialGrid B2bead1 grid-B2.dx potentialGridScale P2bead1 0.5782764 potentialGridScale B2bead1 0.5782764 densityGrid vdw0 grids/1eyg.vdw0.den.dx densityGrid vdw1 grids/1eyg.vdw1.den.dx densityGrid vdw2 grids/1eyg.vdw2.den.dx densityGrid elec grids/1eyg.charge.dx rigidBody ssb2 num 1 mass 48856.4140625 inertia 19375326.0 18923212.0 13511158.0 inputRBCoordinates inputSSBCoords.txt transDamping 779.396325558 757.577520666 735.633430273 rotDamping 3097.88531206 3029.1232551 3548.84746686 gridFile constrain potentials/plane.dx densityGrid constrain den.dx pmfScale constrain 1. gridFile constrain1 sphere.dx densityGrid constrain1 den.dx pmfScale constrain1 1. potentialGrid Pbead2 grid-P.dx potentialGrid Bbead2 grid-B.dx potentialGridScale Pbead2 0.5782764 potentialGridScale Bbead2 0.5782764 potentialGrid P2bead2 grid-P2.dx potentialGrid B2bead2 grid-B2.dx potentialGridScale P2bead2 0.5782764 potentialGridScale B2bead2 0.5782764 potentialGridScale vdw0 1.026964575 potentialGrid vdw0 grids/1eyg.vdw0.pot.dx potentialGridScale vdw1 1.026964575 potentialGrid vdw1 grids/1eyg.vdw1.pot.dx potentialGridScale vdw2 1.026964575 potentialGrid vdw2 grids/1eyg.vdw2.pot.dx potentialGridScale elec 0.5782764 potentialGrid elec grids/1eyg.elec.dx