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Copy path08_A4_B4_reference_system_SIM.txt
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08_A4_B4_reference_system_SIM.txt
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*** TIME INFORMATION ***
Total time: 5.00E-2
dt: 1.00E-8
dt_spring: 1.00E-9
dt_data: 5.00E-4
dt_image: 5.00E-4
*** SYSTEM INFORMATION ***
L_x: 0.1
L_y: 0.1
L_z_out: 0.01
L_z_in: 0.1
Partition Nx: 10
Partition Ny: 10
Partition Nz: 11
*** MOLECULES ***
MOLECULE: "poly_A" Intracellular Number 100 Site_Types 2 Total_Sites 10 Total_Links 9 is2D false
{
TYPE: Name "A" Radius 1.50000 D 2.000 Color MAGENTA STATES "State0"
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
SITE 0 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 1.50000 D 2.000 Color MAGENTA STATES "State0"
x 0.00000 y 41.50000 z 49.50000
SITE 1 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 1.50000 D 2.000 Color MAGENTA STATES "State0"
x 0.00000 y 41.50000 z 58.50000
SITE 2 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 1.50000 D 2.000 Color MAGENTA STATES "State0"
x 0.00000 y 41.50000 z 67.50000
SITE 3 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 52.50000
SITE 4 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 55.50000
SITE 5 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 61.50000
SITE 6 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 64.50000
SITE 7 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 70.50000
SITE 8 : Intracellular : Initial State 'State0'
TYPE: Name "a_linker" Radius 0.75000 D 2.000 Color ORANGE STATES "State0"
x 0.00000 y 41.50000 z 73.50000
SITE 9 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 1.50000 D 2.000 Color MAGENTA STATES "State0"
x 0.00000 y 41.50000 z 76.50000
LINK: Site 0 ::: Site 3
LINK: Site 3 ::: Site 4
LINK: Site 4 ::: Site 1
LINK: Site 1 ::: Site 5
LINK: Site 5 ::: Site 6
LINK: Site 6 ::: Site 2
LINK: Site 2 ::: Site 7
LINK: Site 7 ::: Site 8
LINK: Site 8 ::: Site 9
Initial_Positions: Random
}
MOLECULE: "poly_B" Intracellular Number 100 Site_Types 2 Total_Sites 10 Total_Links 9 is2D false
{
TYPE: Name "B" Radius 1.50000 D 2.000 Color GREEN STATES "State0"
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
SITE 0 : Intracellular : Initial State 'State0'
TYPE: Name "B" Radius 1.50000 D 2.000 Color GREEN STATES "State0"
x 0.00000 y 34.00000 z 38.25000
SITE 1 : Intracellular : Initial State 'State0'
TYPE: Name "B" Radius 1.50000 D 2.000 Color GREEN STATES "State0"
x 0.00000 y 34.00000 z 47.25000
SITE 2 : Intracellular : Initial State 'State0'
TYPE: Name "B" Radius 1.50000 D 2.000 Color GREEN STATES "State0"
x 0.00000 y 34.00000 z 56.25000
SITE 3 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 44.25000
SITE 4 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 53.25000
SITE 5 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 59.25000
SITE 6 : Intracellular : Initial State 'State0'
TYPE: Name "B" Radius 1.50000 D 2.000 Color GREEN STATES "State0"
x 0.00000 y 34.00000 z 65.25000
SITE 7 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 41.25000
SITE 8 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 50.25000
SITE 9 : Intracellular : Initial State 'State0'
TYPE: Name "b_linker" Radius 0.75000 D 2.000 Color PINK STATES "State0"
x 0.00000 y 34.00000 z 62.25000
LINK: Site 0 ::: Site 7
LINK: Site 7 ::: Site 3
LINK: Site 3 ::: Site 1
LINK: Site 1 ::: Site 8
LINK: Site 8 ::: Site 4
LINK: Site 4 ::: Site 2
LINK: Site 2 ::: Site 5
LINK: Site 5 ::: Site 9
LINK: Site 9 ::: Site 6
Initial_Positions: Random
}
*** MOLECULE FILES ***
MOLECULE: poly_A null
MOLECULE: poly_B null
*** CREATION/DECAY REACTIONS ***
'poly_A' : kcreate 0.0 kdecay 0.0
'poly_B' : kcreate 0.0 kdecay 0.0
*** STATE TRANSITION REACTIONS ***
*** ALLOSTERIC REACTIONS ***
*** BIMOLECULAR BINDING REACTIONS ***
'A_B_binding' 'poly_A' : 'A' : 'State0' + 'poly_B' : 'B' : 'State0' kon 20.0 koff 7000.0 Bond_Length 0.5
*** MOLECULE COUNTERS ***
'poly_A' : Measure Total Free Bound
'poly_B' : Measure Total Free Bound
*** STATE COUNTERS ***
'poly_A' : 'A' : 'State0' : Measure Total Free Bound
'poly_A' : 'a_linker' : 'State0' : Measure Total Free Bound
'poly_B' : 'B' : 'State0' : Measure Total Free Bound
'poly_B' : 'b_linker' : 'State0' : Measure Total Free Bound
*** BOND COUNTERS ***
'A_B_binding' : Counted
*** SITE PROPERTY COUNTERS ***
'poly_A' Site 0 : Track Properties true
'poly_A' Site 1 : Track Properties true
'poly_A' Site 2 : Track Properties true
'poly_A' Site 3 : Track Properties true
'poly_A' Site 4 : Track Properties true
'poly_A' Site 5 : Track Properties true
'poly_A' Site 6 : Track Properties true
'poly_A' Site 7 : Track Properties true
'poly_A' Site 8 : Track Properties true
'poly_A' Site 9 : Track Properties true
'poly_B' Site 0 : Track Properties true
'poly_B' Site 1 : Track Properties true
'poly_B' Site 2 : Track Properties true
'poly_B' Site 3 : Track Properties true
'poly_B' Site 4 : Track Properties true
'poly_B' Site 5 : Track Properties true
'poly_B' Site 6 : Track Properties true
'poly_B' Site 7 : Track Properties true
'poly_B' Site 8 : Track Properties true
'poly_B' Site 9 : Track Properties true
*** CLUSTER COUNTERS ***
Track_Clusters: true
*** SYSTEM ANNOTATIONS ***
*** MOLECULE ANNOTATIONS ***
Annotation: 'poly_A'
{
}
Annotation: 'poly_B'
{
}
*** REACTION ANNOTATIONS ***
Annotation: 'A_B_binding'
{
}
*** SIMULATION STATE ***
Runs: 100
Parallel: false
SimultaneousRuns: 1
Aborted: false
IsRunning: false
HasResults: false
RunOnCluster: false
*** PROCESSOR FILES ***
MoleculeAverages: 'null'
BondAverages: 'null'
StateAverages: 'null'
RunningTimes: 'null'
*** RAW DATA FILES ***
'null'
*** SITE DATA FILES ***
null