## Initialization

units real                                                                                 
dimension 3                                                                                
boundary p p p                                                                             
atom_style full                                                                            	
processors * * *

pair_style lj/cut/coul/long 10                                                       
pair_modify mix arithmetic                                                                 
bond_style harmonic                                                                        
angle_style harmonic 
dihedral_style harmonic
improper_style cvff      
special_bonds lj/coul 0 0 0                                                               
kspace_style ewald 0.0001  

neighbor 0.2 bin                                                                                 
neigh_modify delay 0 every 5 check yes   

read_data Initial_m.data 

timestep 1.0
thermo 100
thermo_style custom step vol temp press ke pe evdwl ecoul elong ebond eangle  
log none

## Group

group MMT type <> 1 8
group Na type 9 20
group PAA type <> 10 19
group PAAS type <> 10 20

## Modify

displace_atoms PAAS move 0 0 -13 

## Setting

velocity all create 5 888888 mom yes rot yes dist gaussian loop geom  
velocity MMT set 0 0 0  
fix 1 MMT setforce 0 0 0  

min_style sd                                                  
minimize 1.0e-15 1.0e-15 10000 100000 

fix 2 all shake 0.0001 10 0 b 4 5 10 11 8 13  

## NVT 

fix 3 all nvt temp 5 300 100 
run 10000
write_data Initial_modify.data
unfix 3
reset_timestep 0

fix 4 all nvt temp 300 300 100 

## Output

dump 1 all custom 100 All_Equ.dump id type x y z
dump 2 PAA custom 100 PAA_Equ.dump id type xu yu zu  
dump 3 Na custom 100 Na_Equ.dump id type x y z  
dump 4 all custom 1 All_Test.dump id type x y z 

dump_modify 1 sort id
dump_modify 2 sort id
dump_modify 3 sort id
dump_modify 4 sort id

run 2000000

write_data Initial_modify2.data