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Simulation0_SIM.txt
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*** TIME INFORMATION ***
Total time: 1.00E-2
dt: 1.00E-8
dt_spring: 1.00E-9
dt_data: 1.00E-4
dt_image: 1.00E-4
*** SYSTEM INFORMATION ***
L_x: 0.1
L_y: 0.1
L_z_out: 0.01
L_z_in: 0.09
Partition Nx: 10
Partition Ny: 10
Partition Nz: 10
*** MOLECULES ***
MOLECULE: "R" Membrane Number 5 Site_Types 3 Total_Sites 4 Total_Links 4 is2D false
{
TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0" "State1"
TYPE: Name "L" Radius 1.00000 D 1.000 Color ORANGE STATES "State0"
TYPE: Name "Anchor" Radius 1.00000 D 2.000 Color GRAY STATES "Anchor"
SITE 0 : Intracellular : Initial State 'State0'
TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0" "State1"
x 0.00000 y 17.23333 z 50.15556
SITE 1 : Membrane : Initial State 'Anchor'
TYPE: Name "Anchor" Radius 1.00000 D 2.000 Color GRAY STATES "Anchor"
x 0.00000 y 20.70000 z 37.00000
SITE 2 : Intracellular : Initial State 'State0'
TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0" "State1"
x 0.00000 y 24.41111 z 49.90556
SITE 3 : Intracellular : Initial State 'State0'
TYPE: Name "L" Radius 1.00000 D 1.000 Color ORANGE STATES "State0"
x 0.00000 y 20.89444 z 42.11667
LINK: Site 2 ::: Site 0
LINK: Site 3 ::: Site 1
LINK: Site 3 ::: Site 0
LINK: Site 3 ::: Site 2
Initial_Positions: Random
}
MOLECULE: "Adapter" Intracellular Number 5 Site_Types 2 Total_Sites 3 Total_Links 2 is2D false
{
TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
TYPE: Name "L" Radius 1.00000 D 1.000 Color GOLD STATES "State0"
SITE 0 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
x 0.00000 y 23.13333 z 49.45000
SITE 1 : Intracellular : Initial State 'State0'
TYPE: Name "L" Radius 1.00000 D 1.000 Color GOLD STATES "State0"
x 0.00000 y 22.88889 z 43.77778
SITE 2 : Intracellular : Initial State 'State0'
TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
x 0.00000 y 22.42778 z 37.08333
LINK: Site 0 ::: Site 1
LINK: Site 1 ::: Site 2
Initial_Positions: Random
}
*** MOLECULE FILES ***
MOLECULE: R null
MOLECULE: Adapter null
*** CREATION/DECAY REACTIONS ***
'R' : kcreate 0.0 kdecay 0.0
'Adapter' : kcreate 0.0 kdecay 0.0
*** STATE TRANSITION REACTIONS ***
'TransitionReaction0' :: 'R' : 'R' : 'State0' --> 'State1' Rate 0.0 Condition Bound 'Adapter' : 'A' : 'State0'
*** ALLOSTERIC REACTIONS ***
'AllostericReaction0' :: 'R' : Site 0 : 'State0' --> 'State1' Rate 0.0 Allosteric_Site 2 State 'State0'
*** BIMOLECULAR BINDING REACTIONS ***
'BindingReaction0' 'R' : 'R' : 'Any_State' + 'Adapter' : 'A' : 'Any_State' kon 10.0 koff 10.0 Bond_Length 1.0
*** MOLECULE COUNTERS ***
'R' : Measure Total Free Bound
'Adapter' : Measure Total Free Bound
*** STATE COUNTERS ***
'R' : 'R' : 'State0' : Measure Total Free Bound
'R' : 'R' : 'State1' : Measure Total Free Bound
'R' : 'L' : 'State0' : Measure Total Free Bound
'R' : 'Anchor' : 'Anchor' : Measure Total Free Bound
'Adapter' : 'A' : 'State0' : Measure Total Free Bound
'Adapter' : 'L' : 'State0' : Measure Total Free Bound
*** BOND COUNTERS ***
'BindingReaction0' : Counted
*** SITE PROPERTY COUNTERS ***
'R' Site 0 : Track Properties true
'R' Site 1 : Track Properties true
'R' Site 2 : Track Properties true
'R' Site 3 : Track Properties true
'Adapter' Site 0 : Track Properties true
'Adapter' Site 1 : Track Properties true
'Adapter' Site 2 : Track Properties true
*** CLUSTER COUNTERS ***
Track_Clusters: true
*** SYSTEM ANNOTATIONS ***
*** MOLECULE ANNOTATIONS ***
Annotation: 'R'
{
}
Annotation: 'Adapter'
{
}
*** REACTION ANNOTATIONS ***
Annotation: 'TransitionReaction0'
{
}
Annotation: 'AllostericReaction0'
{
}
Annotation: 'BindingReaction0'
{
}
*** SIMULATION STATE ***
Runs: 1
Parallel: false
SimultaneousRuns: 1
Aborted: false
IsRunning: false
HasResults: true
RunOnCluster: false
*** PROCESSOR FILES ***
MoleculeAverages: 'Simulation0_SIM_AverageMoleculeCounts_0_0.csv'
BondAverages: 'Simulation0_SIM_AverageBondCounts_0_0.csv'
StateAverages: 'Simulation0_SIM_AverageStateCounts_0_0.csv'
RunningTimes: 'RunningTimes.csv'
*** RAW DATA FILES ***
'TOTAL R' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL R.csv'
'FREE R' LOCATION 'Simulation0_SIM_AllData_0_0_FREE R.csv'
'BOUND R' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND R.csv'
'TOTAL Adapter' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL Adapter.csv'
'FREE Adapter' LOCATION 'Simulation0_SIM_AllData_0_0_FREE Adapter.csv'
'BOUND Adapter' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND Adapter.csv'
'BindingReaction0' LOCATION 'Simulation0_SIM_AllData_0_0_BindingReaction0.csv'
'TOTAL R : R : State0' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL R _ R _ State0.csv'
'FREE R : R : State0' LOCATION 'Simulation0_SIM_AllData_0_0_FREE R _ R _ State0.csv'
'BOUND R : R : State0' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND R _ R _ State0.csv'
'TOTAL R : R : State1' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL R _ R _ State1.csv'
'FREE R : R : State1' LOCATION 'Simulation0_SIM_AllData_0_0_FREE R _ R _ State1.csv'
'BOUND R : R : State1' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND R _ R _ State1.csv'
'TOTAL R : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL R _ L _ State0.csv'
'FREE R : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_FREE R _ L _ State0.csv'
'BOUND R : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND R _ L _ State0.csv'
'TOTAL R : Anchor : Anchor' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL R _ Anchor _ Anchor.csv'
'FREE R : Anchor : Anchor' LOCATION 'Simulation0_SIM_AllData_0_0_FREE R _ Anchor _ Anchor.csv'
'BOUND R : Anchor : Anchor' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND R _ Anchor _ Anchor.csv'
'TOTAL Adapter : A : State0' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL Adapter _ A _ State0.csv'
'FREE Adapter : A : State0' LOCATION 'Simulation0_SIM_AllData_0_0_FREE Adapter _ A _ State0.csv'
'BOUND Adapter : A : State0' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND Adapter _ A _ State0.csv'
'TOTAL Adapter : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_TOTAL Adapter _ L _ State0.csv'
'FREE Adapter : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_FREE Adapter _ L _ State0.csv'
'BOUND Adapter : L : State0' LOCATION 'Simulation0_SIM_AllData_0_0_BOUND Adapter _ L _ State0.csv'
*** SITE DATA FILES ***
'R Site 0' LOCATION 'Simulation0_SIM_AverageSiteProperties_R_Site_0_0_0.csv'
'R Site 1' LOCATION 'Simulation0_SIM_AverageSiteProperties_R_Site_1_0_0.csv'
'R Site 2' LOCATION 'Simulation0_SIM_AverageSiteProperties_R_Site_2_0_0.csv'
'R Site 3' LOCATION 'Simulation0_SIM_AverageSiteProperties_R_Site_3_0_0.csv'
'Adapter Site 0' LOCATION 'Simulation0_SIM_AverageSiteProperties_Adapter_Site_0_0_0.csv'
'Adapter Site 1' LOCATION 'Simulation0_SIM_AverageSiteProperties_Adapter_Site_1_0_0.csv'
'Adapter Site 2' LOCATION 'Simulation0_SIM_AverageSiteProperties_Adapter_Site_2_0_0.csv'