error in out range of atoms cannot compute ppm

hello dear
i’m trying to simulate water and cu.timestep was 2 but i got this error “error in out range of atoms cannot compute ppm”.i read the doc so i changed the the time step to .0000025 it worked and next changed to .0025 i got this error"bond atom 86 85 missing on proce 0 step 41".does anybody know what should i do.?
i appreciate any help
thanks
regard

atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

group hydrogen type 1
group water type 1 2
group cu type 3
group oxygen type 2

lattice fcc 3.615 #Cu lattice constant
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu

set group oxygen charge -1.040 #???
set group hydrogen charge .520 #???
set group cu charge 0.000

pair_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes

---------- Relaxation -----------------------------------------

minimization : avoid atoms overlapping

min_style fire
min_modify dmax 0.01
minimize 1.0e-10 0 100000 1000000

---------- output----------------------------------------------

thermo 100
thermo_style custom step etotal enthalpy pe press ke
thermo_modify flush yes

velocity all create 300.0 4928459 rot yes dist gaussian #23482341

fix 1 hydrogen shake 1e-6 500 0 m 1.0 a 1 #for hydrogen
fix 12 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0

---------- compute ----------------------------------------

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom

timestep 0.0025
run 6000