/process/dna/e-SolvationSubType Meesungnoen2002
#/process/dna/e-SolvationSubType Ritchie1994
#/process/dna/e-SolvationSubType Terrisol1990

/run/verbose 1
/control/verbose 0

/world/worldSize 50 um
/cell/radiusSize 14 2.5 14 um
/scheduler/endTime 5.0 ns
/scheduler/maxNullTimeSteps 10000000
/dnageom/radicalKillDistance 9 nm
/dnageom/interactionDirectRange 3.5 angstrom

/dnageom/placementSize 75 75 75 nm
/dnageom/fractalScaling 75 75 75 nm
/dnageom/definitionFile geometries/cube-centred-X-8.txt
/dnageom/placementVolume turn geometries/turned_solenoid_750_withHistone.txt
/dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_750_withHistone.txt true
/dnageom/placementVolume straight geometries/straight_solenoid_750_withHistone.txt
/dnageom/checkOverlaps False

/dnadamage/directDamageLower 5 eV
/dnadamage/directDamageUpper 37.5 eV

/dnadamage/indirectOHBaseChance 1.0
/dnadamage/indirectOHStrandChance 0.405
/dnadamage/inductionOHChance 0.00

/dnadamage/indirectHBaseChance 1.0
/dnadamage/indirectHStrandChance 0.0
/dnadamage/inductionHChance 0.00

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.0
/dnadamage/inductionEaqChance 0.00


/chromosome/add cell ellipse 7100 2500 7100 0 0 0 nm 0 0 0
#/chromosome/add cell sphere 3000 0 0 0 nm

/run/initialize
/run/printProgress 100

# Source Geometry
/gps/pos/type Plane
/gps/pos/shape Circle
/gps/pos/centre 0 3000 0 nm
/gps/pos/rot1 0 0 1 
/gps/pos/rot2 1 0 0 
/gps/pos/radius 7100 nm
/gps/direction 0 -1 0

# Source Energy
/gps/particle  proton
/analysisDNA/fileName 50MeV_linear_5ns
/gps/energy 50 MeV
/run/beamOn 1000
#
/gps/particle  proton
/analysisDNA/fileName 4MeV_linear_5ns
/gps/energy 4 MeV
/run/beamOn 500