# molecular dynamic simulation; chain extended molecule, long spacers
units lj
dimension  3
boundary p p p
atom_style angle
read_data data_long.dat
velocity all create 0.01 23656 dist gaussian

group a1 id 1 973 1945 2917 3889 4861 5833 6805 7777 8749
fix graft a1 setforce 0 0 0

pair_style soft 2
pair_coeff 1 1 0.2
pair_coeff 1 2 0.2
pair_coeff 2 2 0.2

bond_style harmonic
bond_coeff 1 1 1.2

angle_style harmonic
angle_coeff 1 10.0 180


fix 1 all nvt temp 0.1 0.1 0.01
thermo 2000
timestep 0.005
dump 1 all custom 100 ext_chain_long_bnd_no_interaction.md id type xu yu zu
run 6000

special_bonds lj 0.0 0.0 0.0 angle yes

pair_style lj/cut 5.0
pair_coeff 1 1 1 0.5
pair_modify shift yes
pair_coeff 1 2 0.1 0.5 0.561
pair_coeff 2 2 0.1 0.5 0.561

neigh_modify page 100000
neigh_modify one 10000

angle_style harmonic
angle_coeff 1 10.0 180

min_style cg  
minimize 1.0e-4 1.0e-6 10000 100000

restart 500000 restart01.md restart02.md

dump_modify 1 every 40000 
timestep 0.0005
run 100000000