Dear lammps-users
I am trying to create a TIP4P water molecule in LAMMPS by reading my own initial structure with the “read_data" and then using the "create_atoms ". However, I get the following error. Could you help me to find out what’s wrong with my script? Thank you so much!
ERROR: Molecule topology/atom exceeds system topology/atom (src/molecule.cpp:1901)
Last command: create_atoms 0 random 3 34564 water_zone mol water 25367 overlap 1.33
create_water_4.lammps
units real
atom_style full
read_data tob_water_update_4.data &
extra/atom/types 2 &
extra/bond/types 1 &
extra/angle/types 1 &
extra/bond/per/atom 3 &
extra/angle/per/atom 2
molecule water tip3p.mol
pair_style hybrid/overlay lj/cut/tip4p/long 4 5 1 1 0.1546 16 lj/cut 12
bond_style harmonic
angle_style harmonic
kspace_style pppm/tip4p 1.0e-4
mass 4 15.9994 # Water Oxygen
mass 5 1.008 # Water Hydrogen
pair_coeff * * lj/cut/tip4p/long 0.0 0.0
pair_coeff 4 4 lj/cut/tip4p/long 0.185199 3.1589
pair_coeff 1 4 lj/cut 0.0993886 3.211577733
pair_coeff 3 4 lj/cut 0.01794068 3.844182653
pair_coeff 2 5 lj/cut 0.1272912 2.66
pair_coeff 1 5 lj/cut 0.0675658 2.65
pair_coeff 3 5 lj/cut 0.00959296 3.33979572
pair_coeff 2 4 lj/cut 0.163726 3.27333
bond_coeff 1 0 0.9572
angle_coeff 1 0 104.52
region water_zone block 0.0 34.0 0.0 36.0 12.0 22.0 units box
create_atoms 0 random 33 34564 water_zone mol water 25367 overlap 1.33
fix 1 all shake 1.0e-4 20 0 b 1 a 1
group csh type 1 2 3
group water type 4 5
neighbor 2.0 bin
neigh_modify delay 10 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 100
minimize 1.0e-5 1.0e-7 1000 10000
fix 2 all nvt temp 300.0 300.0 100.0
timestep 1.0
run 10000
write_data csh_with_water.data
tip3p.mol
Water molecule. TIP3P geometry
3 atoms
2 bonds
1 angles
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 4 # O
2 5 # H
3 5 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2
tob_water_update_4.data
LAMMPS-data file written from a jupyter notebook, 04_fill_H2O_betw_tobs.ipynb.
1680 atoms
0 bonds
0 angles
3 atom types
0.0 34.050 xlo xhi
0.0 36.500 ylo yhi
0.0 34.078 zlo zhi
Masses
1 40.078
2 15.9994
3 28.085
Atoms # atom-ID molecule-ID atom-type q x y z ? ? ?
1 0 1 1.6800 8.553 2.738 26.430
2 0 1 1.6800 0.036 4.563 28.437
*tob_water_update_4.data is only partially posted