False out of bounds error, and then simulation abort

[jonathanfischer97]

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