## 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 1                                                               
kspace_style ewald 0.0001  

neighbor 0.2 bin                                                                                 
neigh_modify delay 0 every 5 check yes   

read_data Initial.data 

timestep 0.5
thermo 100
thermo_style custom step temp ke pe pzz lz
log none

## Group

group MMT type <> 1 8
group Na type 9 22
group PAA type <> 12 21
group InterWater type 10 11
#group Other subtract all MMT InterWater

## 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 3 5 6 11 12 a 4

## Heat and NPT 

fix 3 all nvt temp 5 300 $(100*dt)

dump 1 all custom 100 All.dump id type x y z

run 2000

unfix 3

fix 4 all npt temp 300 300 $(100*dt) z 1 1 $(1000*dt) #dilate Other

run 5000000
a
## NVT

unfix 4
reset_timestep 0

fix 5 all nvt temp 300 300 $(100*dt)

compute 1 PAA com 

## Output

thermo_style custom step temp ke pe c_1[1] c_1[2] c_1[3] 

dump 2 all custom 100 All_Equ.dump id type x y z
dump 3 PAA custom 100 PAA_Equ.dump id type x y z  
dump 4 Na custom 100 Na_Equ.dump id type x y z  
dump 5 InterWater custom 100 InterWater_Equ.dump id type x y z  
dump 6 PAA custom 100 PAA_unwrap.dump id type xu yu zu 

dump_modify 1 sort id
dump_modify 2 sort id
dump_modify 3 sort id
dump_modify 4 sort id
dump_modify 5 sort id
dump_modify 6 sort id

run 200000000

write_data PAAS_MMT_Dry.data