False out of bounds error, and then simulation abort #4
Description
Seemingly incorrect out of bounds error
Got this in the initial output of a simulation after it aborted itself:
...
Molecule 1 is outside simulation volume with center of mass coordinates [ -63.8805 81.449 -250]. Attempting to fit back into box.
Attempting to put complex 1 back into simulation volume...
Comcoords: -63.8805 81.449 -250
Member list: 1
D: 1 1 0
Dr: 0 0 0
Molecule 1 is outside simulation volume with center of mass coordinates [ -63.8805 81.449 -250]. Attempting to fit back into box.
Attempting to put complex 1 back into simulation volume...
Comcoords: -63.8805 81.449 -250
Member list: 1
D: 1 1 0
Dr: 0 0 0
Cannot fit complex 1 into simulation volume. Exiting...
According to my waterbox dimesions, those coordinates shouldn't be out of bounds:
start parameters
nItr = 100000000 # Total number of simulation iterations
timeStep = 10 # Duration of each iteration (μs)
timeWrite = 100 # Iteration interval to write _time.dat statistics files
trajWrite = 200000000 # Iteration interval to write coordinates to trajectory.xyz
restartWrite = 200000 # Iteration interval to overwrite restart.dat
checkPoint = 5000000 # Iteration interval to write separate restart_N.dat files
pdbWrite = 100000 # Iteration interval to write individual PDB files
end parameters
start boundaries
WaterBox = [166.9, 166.9, 500.0] # Dimensions (nm) calculated based on DF
end boundaries
start molecules
# Initial counts calculated from dataset concentrations
lipid : 603 (head~U) 0 (head~P)
adaptor : 182
kinase : 262
phosphatase : 102
end molecules
...
Should be noted though that this issue doesn't happen everytime I don't think, with repeat or replicate simulations running longer or to completion without the above issue.
Full simulation files to reproduce the issue:
parms.inp
start parameters
nItr = 100000000 # Total number of simulation iterations
timeStep = 10 # Duration of each iteration (μs)
timeWrite = 100 # Iteration interval to write _time.dat statistics files
trajWrite = 200000000 # Iteration interval to write coordinates to trajectory.xyz
restartWrite = 200000 # Iteration interval to overwrite restart.dat
checkPoint = 5000000 # Iteration interval to write separate restart_N.dat files
pdbWrite = 100000 # Iteration interval to write individual PDB files
end parameters
start boundaries
WaterBox = [167.2, 167.2, 2000.0] # Dimensions (nm) calculated based on DF
end boundaries
start molecules
# Initial counts calculated from dataset concentrations
lipid : 1103 (head~U) 0 (head~P)
adaptor : 102
kinase : 665
phosphatase : 202
end molecules
start reactions
################################
### Kinase - Lipid Interaction ###
################################
# L + K <-> LK -> K + Lp
kinase(lbs) + lipid(head~U) <-> kinase(lbs!1).lipid(head~U!1)
onRate3Dka = 0.004035401267816 # kfᴸᴷ nm³/μs
offRatekb = 230.849880049839697 # krᴸᴷ s⁻¹
kcat = 184.379495460832914 # kcatᴸᴷ s⁻¹
norm1 = [0,0,1]
norm2 = [0,0,1]
assocAngles = [1.5707963, 1.5707963, nan, nan, M_PI]
sigma = 1.0
length3Dto2D = 1.0
coupledRxnLabel = PhosphorylationByKinase
# Catalytic Step Definition: LK -> K + Lp
lipid(head~U) -> lipid(head~P)
rate = 0.0 # Driven by coupling
rxnLabel = PhosphorylationByKinase
###################################
### Phosphatase - Lipid Interaction ###
###################################
# Lp + P <-> LpP -> P + L
phosphatase(lbs) + lipid(head~P) <-> phosphatase(lbs!1).lipid(head~P!1)
onRate3Dka = 0.941633553558047 # kfᴸᴾ nm³/μs
offRatekb = 0.812120409102941 # krᴸᴾ s⁻¹
kcat = 9.539543373198804 # kcatᴸᴾ s⁻¹
norm1 = [0,0,1]
norm2 = [0,0,1]
assocAngles = [1.5707963, 1.5707963, nan, nan, M_PI]
sigma = 1.0
length3Dto2D = 1.0
coupledRxnLabel = DephosphorylationByPhosphatase
# Catalytic Step Definition: LpP -> P + L
lipid(head~P) -> lipid(head~U)
rate = 0.0 # Driven by coupling
rxnLabel = DephosphorylationByPhosphatase
#################################
### Adaptor - Lipid Interaction ###
#################################
# Lp + A <-> LpA
lipid(head~P) + adaptor(lbs) <-> lipid(head~P!1).adaptor(lbs!1)
onRate3Dka = 0.867439711213740 # kfᴸᴬ nm³/μs
offRatekb = 1.877592404083814 # krᴸᴬ s⁻¹
norm1 = [0,0,1]
norm2 = [0,0,1]
assocAngles = [1.5707963, 1.5707963, nan, nan, M_PI]
length3Dto2D = 1.0
sigma = 1.0
############################################
### Adaptor - Enzyme Interactions (Membrane) ###
############################################
# LpA + K <-> LpAK
kinase(abs) + adaptor(ebs,lbs!*) <-> kinase(abs!1).adaptor(ebs!1,lbs!*)
onRate3Dka = 0.001806133322997 # kfᴬᴷ nm³/μs
offRatekb = 0.007128944714605 # krᴬᴷ s⁻¹
norm1 = [0,0,1]
norm2 = [0,0,1]
assocAngles = [1.5707963, 2.35619, nan, M_PI, M_PI]
length3Dto2D = 1.0
sigma = 1.0
# LpA + P <-> LpAP
phosphatase(abs) + adaptor(ebs,lbs!*) <-> phosphatase(abs!1).adaptor(ebs!1,lbs!*)
onRate3Dka = 1.373099562951463 # kfᴬᴾ nm³/μs
offRatekb = 3.481589883103652 # krᴬᴾ s⁻¹
norm1 = [0,0,1]
norm2 = [0,0,1]
assocAngles = [1.5707963, 2.35619, nan, M_PI, M_PI]
length3Dto2D = 1.0
sigma = 1.0
end reactions
lipid.mol
##
# lipid molecule information file
##
Name = lipid
isLipid = true
checkOverlap = false
# translational diffusion constants
D = [1.0, 1.0, 0.0]
# rotational diffusion constants
Dr = [0, 0, 0]
# Coordinates
COM 0.0000 0.0000 0.0000
head 0.0000 0.0000 1.0000
bonds = 1
com head
state = head~U~P
adaptor.mol
##
# adaptor molecule information file
##
Name = adaptor
checkOverlap = false
# translational diffusion constants
D = [25.0,25.0,25.0]
# rotational diffusion constants
Dr = [0.5,0.5,0.5]
# Coordinates, with states below, or
COM 0.0000 0.0000 0.0000
lbs 0.0000 0.0000 -2.0000
ebs 0.0000 1.0000 -1.0000
bonds = 3
com lbs
com ebs
kinase.mol
##
# PIP5K molecule information file
# phosphorylates PI(4)P to PI(4,5)P2
##
Name = kinase
checkOverlap = false
# translational diffusion constants
D = [25.0,25.0,25.0]
# rotational diffusion constants
Dr = [0.5,0.5,0.5]
# Coordinates, with states below, or
COM 0.0000 0.0000 0.0000
abs 0.0000 0.0000 0.5000
lbs 0.0000 0.0000 -0.5000
bonds = 2
COM abs
COM lbs
phosphatase.mol
##
# synaptojanin molecule information file
# dephosphorylates PI(4,5)P2 to PI(4)P
##
Name = phosphatase
checkOverlap = false
# translational diffusion constants
D = [25.0,25.0,25.0]
# rotational diffusion constants
Dr = [0.5,0.5,0.5]
# Coordinates, with states below, or
COM 0.0000 0.0000 0.0000
abs 0.0000 0.0000 0.5000
lbs 0.0000 0.0000 -0.5000
bonds = 2
COM abs
COM lbs