Gabriele Cosmo
108 lines
2.8 KiB
Plaintext
108 lines
2.8 KiB
Plaintext
### E. coli bacterium
|
|
|
|
#
|
|
# See more details on moleculardna specific UI commands:
|
|
# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
|
|
# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
|
|
# - the README file
|
|
# - the messenger classes of the moleculardna example
|
|
#
|
|
|
|
# Verbosity: settings
|
|
/control/verbose 1
|
|
/run/verbose 2
|
|
/dnageom/verbose 1
|
|
#/tracking/verbose 2
|
|
|
|
# Chemistry: selection of IRT_syn
|
|
/process/chem/TimeStepModel IRT_syn
|
|
|
|
# Chemistry: activation
|
|
/chem/activate true
|
|
|
|
# Chemistry: verbosity
|
|
/scheduler/verbose 0
|
|
|
|
# Chemistry: end time of chemistry stage
|
|
/scheduler/endTime 1 us
|
|
|
|
# Geometry: size of World volume
|
|
/world/worldSize 8 um
|
|
|
|
# Geometry: optimisation of voxelisation
|
|
/dnageom/setSmartVoxels 1
|
|
|
|
# Geometry: creation
|
|
# See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
|
|
# - Side length for each placement
|
|
/dnageom/placementSize 50 50 50 nm
|
|
# - Scaling of XYZ in fractal definition file
|
|
/dnageom/fractalScaling 50 50 50 nm
|
|
# - Path to file that defines placement locations
|
|
/dnageom/definitionFile geometries/bacteria-XFXFXFX-4.txt
|
|
# - Set placement volumes
|
|
/dnageom/placementVolume turn geometries/8strands_50nm_turn.txt
|
|
/dnageom/placementVolume turntwist geometries/8strands_50nm_turn.txt true
|
|
/dnageom/placementVolume straight geometries/8strands_50nm_straight.txt
|
|
|
|
# Geometry: distance from base pairs at which radicals are killed
|
|
/dnageom/radicalKillDistance 4 nm
|
|
|
|
# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
|
|
/dnageom/interactionDirectRange 6 angstrom
|
|
|
|
# Damage: model settings
|
|
/dnadamage/directDamageLower 17.5 eV
|
|
/dnadamage/directDamageUpper 17.5 eV
|
|
|
|
/dnadamage/indirectOHBaseChance 1.0
|
|
/dnadamage/indirectOHStrandChance 0.4
|
|
/dnadamage/inductionOHChance 0.
|
|
|
|
/dnadamage/indirectHBaseChance 1.0
|
|
/dnadamage/indirectHStrandChance 0.4
|
|
/dnadamage/inductionHChance 0.0
|
|
|
|
/dnadamage/indirectEaqBaseChance 1.0
|
|
/dnadamage/indirectEaqStrandChance 0.4
|
|
/dnadamage/inductionEaqChance 0.0
|
|
|
|
# Analysis: add ellipsoid chromosomal region of interest, with the name "bacteria"
|
|
/chromosome/add bacteria ellipse 900 400 400 0 0 0 nm 0 0 0
|
|
|
|
# Analysis: save plot data to specified file
|
|
#/chromosome/plotData chromosome.txt
|
|
|
|
# Tests of geometry
|
|
#/dnatests/chromosome
|
|
|
|
# Analysis: save strands in given directory
|
|
/analysisDNA/saveStrands false
|
|
/analysisDNA/strandDir ./damage_maps/
|
|
|
|
# Run: initialization
|
|
/run/initialize
|
|
|
|
# Tests of geometry
|
|
/dnatests/uniqueid
|
|
/dnatests/basepairs
|
|
|
|
# Run: progress display
|
|
/run/printProgress 1
|
|
|
|
# Source geometry
|
|
/gps/pos/type Surface
|
|
/gps/pos/shape Ellipsoid
|
|
/gps/pos/centre 0 0 0 nm
|
|
/gps/pos/halfx 900 nm
|
|
/gps/pos/halfy 400 nm
|
|
/gps/pos/halfz 400 nm
|
|
/gps/ang/type cos
|
|
|
|
# Source particle and energy
|
|
/gps/particle e-
|
|
/gps/energy 9.999 keV
|
|
|
|
# Beam on
|
|
/run/beamOn 500
|