Dear LAMMPS users,
I prepared a data file for sodium chloride solution with mole template. I defined potential of water and ions with pair_style lj/charmm/coul/long 8.0 10.0. Although I minimized system, some bond of water molecules are missing at the beginning. Any suggestions?
echo both
units metal
atom_style full
bond_style harmonic
angle_style charmm
read_restart min
neigh_modify delay 0 every 1 check yes
------------------------------- group -------------------------------
group oxygen type 1
group hydrogen type 2
group water type 1 2
group Na type 3
group Cl type 4
group ions type 3 4
------------------------------- potential -------------------------------
pair_style lj/charmm/coul/long 8.0 10.0 7 9
pair_coeff 1 1 0.00673885 3.169
pair_coeff 2 2* 0.00000 0.00000
pair_coeff 1 2 0.00000 0.00000
pair_coeff 3 3 0.004336412 2.583
pair_coeff 4 4 0.004336412 4.4
pair_coeff 1 3 0.0054 2.8760
pair_coeff 1 4 0.0054 3.7845
pair_coeff 3 4 0.004336412 3.3302
velocity all create 300.0 12345678 dist gaussian
kspace_style pppm 4.3e-6
special_bonds charmm
bond_coeff 1 19.51 0.9572
angle_coeff 1 2.39 104.52 0 0
fix fxnvt all nvt temp 300.0 300.0 100.0
------------------------------- minimization -------------------------------
min_style fire
minimize 0 0 100000 1000000
write_restart min
------------------------------- Deletion -------------------------------
delete_atoms overlap 1.5 water ions mol yes
------------------------------- run -------------------------------
timestep 1.0
dump 1 all custom 100 traj_nvt.lammpstrj id mol type x y z ix iy iz
dump 2 ions custom 100 traj_nvt_ion.lammpstrj id mol type x y z ix iy iz
thermo 100
run 50000