# 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 0.1 23656 dist gaussian

pair_style lj/cut 20
pair_coeff 1 1 0.1 1.0
pair_modify shift yes
pair_coeff 1 2 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 1.122

bond_style harmonic
bond_coeff 1 1 1.2

angle_style harmonic
angle_coeff 1 10 180
angle_coeff 2 0.0 180

group Ree id 4 5 6
group Ree id 1009 1010 1011

fix 1 all nvt temp 0.1 0.1 0.1
timestep 0.00005
thermo 2000

dump 1 all custom 10000 ext_chain_long_bnd_no_interaction.md id type xu yu zu
dump 2 Ree custom 10000 end_to_end.md id type xu yu zu

run 300000000