ERROR on proc 0: Angle atoms 14337 14336 14338 missing on proc 0 at step 5

Dear Lammps User,

When I am simulating my input file I am getting the following error

ERROR on proc 0: Angle atoms 14337 14336 14338 missing on proc 0 at step 5 (src/ntopo_angle_partial.cpp:69)
Last command: run 40000

My input file is as shown below:

units real
dimension 3
boundary p p p
atom_style full
kspace_style pppm 1.0e-4

read_data 4nmPore.data
#read_restart 3nmPore-200000.restart

group ca type 1
group ox type 2
group hy type 3
group wo type 4
group wh type 5
group hydroxid type 2 3
group ca-o type 1 2
group spc type 4 5
group portlandite type 1 2 3

#delete_atoms group portlandite

pair_style lj/cut/coul/long 10
pair_coeff 1 1 5.0298e-6 5.5617 # ca-ca
pair_coeff 1 2 8.841e-4 4.3636 # ca-o port
pair_coeff 2 2 0.1554 3.1655 # o-o port
pair_coeff 2 3 0.0 0.0 # o-h port
pair_coeff 3 3 0.0 0.0 # h-h port
pair_coeff 4 4 0.1554 3.1655 # o-o water
pair_coeff 5 5 0.0 0.0 # h-h water
pair_coeff 2 4 0.1554 3.1655 # o-o port-water
pair_coeff 1 4 0.0777 4.19586 # ca-o port-water
pair_coeff 1 5 0.0 0.0 # ca-h port-water
pair_coeff 2 5 0.0 1.5827 # o-h port-water
pair_coeff 3 4 0.0 1.5827 # h-h port-water
pair_coeff 3 5 0.0 0.0 # o-h water

bond_style harmonic
bond_coeff 1 554.1349 1.0 # o-h port
bond_coeff 2 554.1349 1.0 # o-h water

angle_style harmonic
angle_coeff 1 30.0 109.47 # ca-o port
angle_coeff 2 45.7696 109.47 # o-h water

#velocity all create 300.0 104112 dist gaussian # From Cygan et.al

#minimize 1.0e-4 1.0e-6 100 1000

neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes one 3000

variable dz equal 0.2
variable zlow equal zlo
variable zhigh equal zhi

compute 5 all ke # Kinetic energy for all the atoms
compute 6 all pe # Potential energy for all the atoms
compute myTemp all temp # Temperature of all the atoms
#compute RDFHydroxidNVT hydroxid rdf 50

region pore block EDGE EDGE EDGE EDGE EDGE EDGE
#delete_atoms group portlandite

fix constrain spc shake 1.0e-4 100 0 b 1 a 1
#fix 2 portlandite setforce 0.0 0.0 0.0
fix 1 all nvt temp 300.0 300.0 500
#fix_modify 1 temp myTemp
fix 5 all ave/time 1 1 500 c_5 file ek.txt
fix 6 all ave/time 1 1 500 c_6 file ep.txt
fix 7 all ave/time 1 1 500 c_myTemp file T.txt
#fix avrdf3 hydroxid ave/time 1 1 10000 c_RDFHydroxidNVT file rdfHydroxid-17-2-15.txt mode vector
#fix densityWaterNVT spc ave/spatial 1 100 100000 z lower {dz} density/mass region pore file densityProfileWater.txt #fix densityHNVT wh ave/spatial 1 100 100000 z lower {dz} density/mass region pore file densityProfileHydrogen.txt
#fix densityOxNVT wo ave/spatial 1 100 100000 z lower ${dz} density/mass region pore file densityProfileOxygen.txt

thermo 100
thermo_style custom step c_myTemp
thermo_modify norm no flush yes

dump NVTDump all custom 50 water-.txt id type mol x y z vx vy vz
restart 100000 4nmPore-
.restart # Remember to collect these in the bash script

timestep 1.0
run 40000

Let me also know if there is any mistake in my input file.

Regards,
Rajneesh

Dear Lammps User,

When I am simulating my input file I am getting the following error

ERROR on proc 0: Angle atoms 14337 14336 14338 missing on proc 0 at step 5 (src/ntopo_angle_partial.cpp:69)
Last command: run 40000

[…]

Let me also know if there is any mistake in my input file.

sorry, but it is not the job of the mailing list to look for errors in your input. it is your job.

that said, the error message you have indicates that you are starting from either a very high potential energy configuration or have an error in your forcefield parameters or topology data.

in the first case, it would help if you would do a minimization before starting with an MD run.
in the other cases, you have to correct the mistake, but it is impossible to tell where that is from remote.

axel.