Dear Steve,
Thank you for your reply. The following is my input script and data file. Please check them.
in.try:
2-d Colloidal anions with small counterions.
#initialization section
units lj #default
dimension 3
boundary p p f
atom_style hybrid charge bond
bond_style harmonic
pair_style lj/cut/coul/cut 2.5 5.0
atom definition section by reading data files
read_data data.gel
bond_coeff 1 1.0 1.0
LJ potentials #epslong sigma cutoff
pair_coeff 1 1 1.0 1.0 1.0 # 5.61230
pair_coeff 2 2 1.0 1.0 1.0 # 1.12246
pair_coeff 1 2 1.0 1.0 1.0
pair_modify shift yes
kspace_style pppm 0.001
kspace_modify slab 3.0
#setting simulation parameters
neighbor 1.5 bin
neigh_modify check yes
define groups
initial velocities
velocity all create 1.0 482748 #generate temperature by random seed
fix 1 all nve
fix 2 all enforce2d
fix 3 all temp/rescale 1000 1.0 1.0 0.02 0.5
Run
timestep 0.003
thermo 500
thermo_style custom step temp press pe ke ecoul elong epair
dump 1 all atom 50 dump.NVE
run 50000
write_restart restart.afterNVE.*