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timestep 2e-05
steps 10000000000
numberFluct 0 # deprecated
interparticleForce 1 # other values deprecated
fullLongRange 0 # deprecated
temperature 291
ParticleDynamicType Langevin
RigidBodyDynamicType Langevin
ParticleLangevinIntegrator BAOAB
outputPeriod 10000.0
## Energy doesn't actually get printed!
outputEnergyPeriod 100000.0
outputFormat dcd
## Infrequent domain decomposition because this kernel is still very slow
decompPeriod 1000
cutoff 35
pairlistDistance 25
origin -1500.0 -1500.0 -1500.0
systemSize 3000 3000 3000
particle B
num 500
mass 181.1
transDamping 1240 1240 1240
gridFile combine.dx
gridFileScale 500
rigidBodyPotential Bbead
particle P
num 500
mass 160.1
transDamping 1240 1240 1240
gridFile combine.dx
gridFileScale 500
rigidBodyPotential Pbead
## Input coordinates
inputParticles trombone-ssb.coords.txt
## 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/trombone-dna-nb.B-B.dat
tabulatedFile 0@1@potentials/trombone-dna-nb.B-P.dat
tabulatedFile 1@1@potentials/trombone-dna-nb.P-P.dat
tabulatedBondFile two_bead_model/BPB.dat
# tabulatedBondFile two_bead_model/BPP.dat
tabulatedBondFile BPP.dat
tabulatedBondFile two_bead_model/BBP.dat
tabulatedAngleFile two_bead_model/p1p2b2.dat
tabulatedAngleFile two_bead_model/p1p2p3.dat
tabulatedAngleFile two_bead_model/b1p2b2.dat
tabulatedAngleFile two_bead_model/b1p2p3.dat
tabulatedDihedralFile two_bead_model/b1p2p3b3.dat
tabulatedDihedralFile two_bead_model/b1p1p2b2.dat
tabulatedDihedralFile two_bead_model/p0p1p2p3.dat
inputRestraints potentials/trombone-dna.restraint.txt
inputBonds potentials/trombone-dna.bonds.txt
inputAngles potentials/trombone-dna.angles.txt
inputDihedrals potentials/trombone-dna.dihedrals.txt
inputExcludes potentials/trombone-dna.exculsions.txt
## RigidBodies
rigidBodyGridGridPeriod 20
rigidBody ssb
num 14
mass 48856.41410648823
inertia 19375322.0 18923208.0 13511100.0
inputRBCoordinates trombone-ssb.rbcoords.txt
transDamping 779.075531386 757.10491996 735.261090254
rotDamping 3096.68320292 3027.72621629 3547.0215724
potentialGrid Pbead grid-P.dx
potentialGrid Bbead grid-B.dx
potentialGridScale Pbead 0.57827709
potentialGridScale Bbead 0.57827709
densityGrid vdw0 grids/1eyg.vdw0.den.dx
potentialGridScale vdw0 1.026964575
potentialGrid vdw0 grids/1eyg.vdw0.pot.dx
densityGrid vdw1 grids/1eyg.vdw1.den.dx
potentialGridScale vdw1 1.026964575
potentialGrid vdw1 grids/1eyg.vdw1.pot.dx
densityGrid vdw2 grids/1eyg.vdw2.den.dx
potentialGridScale vdw2 1.026964575
potentialGrid vdw2 grids/1eyg.vdw2.pot.dx
densityGrid elec grids/1eyg.charge.dx
potentialGridScale elec 0.57827709
potentialGrid elec grids/1eyg.elec.dx
gridFile vdw0 combine.dx
pmfScale vdw0 10