Bond atom missing error

LAMMPS LAMMPS Beginners
1

Hi,

Can you please help me to solve the issue? I am simulating clay-water system, it runs perfectly by 240 water molecules but when I increase the number of water molecules to 480, it shows me the following error:
ERROR on proc 22: Bond atoms 2667 2668 missing on proc 22 at step 43 (src/ntopo_bond_all.cpp:61)

I appreciate it if you could help me. Here is my input file:

units real
boundary p p p
atom_style full
neighbor   1.0 bin
neigh_modify every 1 delay 0 check yes
pair_style lj/cut/coul/long 12.0
kspace_style ewald 0.0001


pair_modify mix arithmetic 

bond_style harmonic
angle_style harmonic

read_data project_Hydrated_CLAY.data

bond_coeff * 554.1349 1.0
angle_coeff * 45.7696  109.47
# Initial Temperature
variable 		T equal 100

# Final Temperature
variable 		TF equal 300

timestep 1.0

thermo	1000

thermo_style	custom step temp pxx pyy pzz pxz pxy pyz ebond eangle epair evdwl etotal lx ly lz vol density  press

group layer1 molecule 1
group layer2 molecule 2
group sodium type 1
fix 333 layer1 spring/self  10
fix 334 layer2 spring/self  10
#fix 335 sodium spring/self  10
##### energy minimization ##################
minimize 	      1.0e-12 1.0e-12 50000 50000
velocity 	      all create $T 61673
velocity 	      all zero linear

############## Equilibration ###########################
dump	      45 all dcd 500 equlibration.dcd
dump	      44 all dcd 500 unwrapequlibration.dcd
dump_modify   44 unwrap yes

fix     69 all  nvt temp   ${TF}   ${TF}   100 
run         1000000
unfix       69

unfix 333
unfix 334
#unfix 335


write_data opt.data
write_restart opt.rest

fix 334 layer2 spring/self  10

fix         69 all  npt temp   ${TF}   ${TF}   100   x 0 0 1000  y 0 0 1000   z 0 20 1000  
run         200000
unfix       69

fix         69 all  npt temp   ${TF}   ${TF}   100   x 0 0 1000  y 0 0 1000   z 20 20 1000  
run         200000
unfix       69

fix         69 all  npt temp   ${TF}   ${TF}   100   x 0 0 1000  y 0 0 1000   z 20 0 1000  
run         200000
unfix       69

fix         69 all  npt temp   ${TF}   ${TF}   100   x 0 0 1000  y 0 0 1000   z 0 0 1000  
run         200000
unfix       69

undump  44
undump  45


write_data bilayer.data
write_restart bilayer.rest
2

Do you have somebody that can advise you on general best practices in MD simulations? Somebody to discuss your simulations with?

There are multiple possible issues that look like beginner mistakes:

  • you seem to be using far too many processors for rather small system. Have you made a scaling test?
  • you are using kspace style ewald instead of pppm. Have you checked which one is faster?
  • you are using a timestep of 1.0fs, which is generally considered too large for a system containing (light and fast) hydrogen atoms without constraints. Have you checked which bonds are affected? Do they include hydrogens? Are they part of a water molecule?
  • most water models used in the kind of simulation you are doing would be rigid models. Which model are you using exactly? Is it a rigid model? If yes, why don’t treat is as a rigid model in your input?
  • have you checked your simulation setup for conserving energy versus the timestep in use?