Gabriele Cosmo
125 lines
3.4 KiB
Plaintext
125 lines
3.4 KiB
Plaintext
### Plasmid default geometry
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#
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# See more details on moleculardna specific UI commands:
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
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# - the README file
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# - the messenger classes of the moleculardna example
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#
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# Physics: choice of thermalization model
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/process/dna/e-SolvationSubType Meesungnoen2002
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#/process/dna/e-SolvationSubType Ritchie1994
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#/process/dna/e-SolvationSubType Terrisol1990
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# Verbosity: settings
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/run/verbose 2
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/tracking/verbose 0
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/control/verbose 1
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/dnageom/verbose 1
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# Chemistry: selection of IRT_syn
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/process/chem/TimeStepModel IRT_syn
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# Chemistry: activation
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/chem/activate true
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# Chemistry: verbosity
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/scheduler/verbose 0
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# Material: verbosity
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/material/verbose 2
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# Geometry: size of World volume
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/world/worldSize 4.84 um
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# Geometry: optimisation of voxelisation
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/dnageom/setSmartVoxels 1
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/dnageom/checkOverlaps false
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# Geometry: creation
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
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# - Side length for each placement
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/dnageom/placementSize 200 200 200 nm
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# - Scaling of XYZ in fractal definition file
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/dnageom/fractalScaling 1 1 1 nm
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# - Path to file that defines placement locations
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/dnageom/definitionFile geometries/prisms_plasmids_positions_500ngpul.txt
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# - Set placement volumes
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/dnageom/placementVolume prism geometries/plasmid_4367.txt
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# Geometry: take the angles in the voxel placement file as multiples of pi
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/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false
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# Geometry: enable custom molecule sizes
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/dnageom/useCustomMoleculeSizes false
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# Geometry: draw cell/chromosome volumes rather than DNA
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/dnageom/drawCellVolumes false
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# Geometry: distance from base pairs at which radicals are killed
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/dnageom/radicalKillDistance 9 nm
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# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
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/dnageom/interactionDirectRange 5.5 angstrom
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# Geometry: activate Histone scavenging function
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/dnageom/activateHistoneScavenging true
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# Analysis: add box chromosomal region of interest, with the name "plasmid"
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/chromosome/add plasmid box 2.21 2.21 2.42 0 0 0 um
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# Damage: model settings
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/dnadamage/directDamageLower 17.5 eV
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/dnadamage/directDamageUpper 17.5 eV
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/dnadamage/indirectOHBaseChance 1.0
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/dnadamage/indirectOHStrandChance 0.65
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/dnadamage/inductionOHChance 0.0
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/dnadamage/indirectHBaseChance 1.0
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/dnadamage/indirectHStrandChance 0.65
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/dnadamage/inductionHChance 0.00
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/dnadamage/indirectEaqBaseChance 1.0
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/dnadamage/indirectEaqStrandChance 0.65
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/dnadamage/inductionEaqChance 0.00
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# Analysis: set whether strands ought be saved
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/analysisDNA/saveStrands false
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# Analysis: gap between DNA fragments in base pair
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# Set to zero to score placement volumes independently
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/analysisDNA/fragmentGap 0 # do not join
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# Draw cell/chromosome volumes rather than DNA (makes DNA invisible)
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/dnageom/drawCellVolumes false
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# Run: initialization
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/run/initialize
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# --> Unit tests
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#/dnatests/uniqueid
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#/dnatests/basepairs
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#/dnatests/chromosome
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#/analysisDNA/testClassifier
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# --> End unit tests
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# Run: progress display
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/run/printProgress 100
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# Source geometry
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/gps/pos/type Plane
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/gps/pos/shape Square
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/gps/pos/centre 0 0 -2.42 um
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/gps/pos/halfx 2.21 um
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/gps/pos/halfy 2.21 um
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# Source particle, energy and angular distribution
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/gps/particle proton
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/gps/energy 3 MeV
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/gps/direction 0 0 1
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# Beam on
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/run/beamOn 10 |