units  real
atom_style full
boundary        p p f

pair_style lj/class2/coul/long 10 15
dielectric      1.0  
bond_style      class2
angle_style     class2
dihedral_style  class2
improper_style  class2
kspace_style pppm 0.0001
kspace_modify slab 3.0


read_data Polymer.data 


#group hydrophobic and hydrophilic

group phyl type 3 4 6 7

group phob type 1 2 5


#fix wall on top and bottom

fix wallphob phob wall/lj93 zhi EDGE 0.25 3.2 15 zlo EDGE 0.25 3.2 15

fix wallphyl phyl wall/lj93 zhi EDGE 1.5 3.2 15  zlo EDGE 1.5 3.2 15

fix_modify wallphob energy yes
fix_modify wallphyl energy yes

neighbor        2.0 bin
neigh_modify every 1 page 150000 one 5000


#minimize

minimize 1.0e-6 1.0e-6 5000 5000


velocity        all create 300.0 497 dist gaussian


thermo 100
thermo_style custom step temp epair emol etotal press vol density
timestep        1.0  # femtoseconds

restart 50000 rst.lambda0

write_data Polymer_min.data

# saving trajectory

dump  Datom all custom 1000 dump.lambda0 id type xu yu zu ix iy iz
dump_modify Datom sort 1

dump  Datom1 all custom 1000 dump.lambda1 id type x y z ix iy iz
dump_modify Datom1 sort 1

#write_dump all custom initial.lammpstrj id type xu yu zu ix iy iz modify sort id
#write_dump all custom initial_wrap.lammpstrj id type x y z ix iy iz modify sort id

#nvt run

fix nvt1 all nvt temp 300 300 50
run 500000
unfix nvt1

#annealing

# equilibration 

label loop
variable loop_ctr loop 5

fix nvt1 all nvt temp 300.0 600.0 50
run 50000 
unfix nvt1

fix nvt2 all nvt temp 600 600 50
run 50000
unfix nvt2

fix nvt3 all nvt temp 600 300 50
run 50000
unfix nvt3

next loop_ctr
jump SELF loop

#nvt run

fix nvt1 all nvt temp 300 300 50
run 200000
unfix nvt1

#npt run

fix npt1 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 1500000
unfix npt1