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# stick a buckyball into a nanotube
units real
dimension 3
boundary f f f
atom_style molecular
newton off
processors * * 1
# read topology
read_data data.bucky-plus-cnt
pair_style lj/cut/gpu 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
special_bonds lj/coul 0.0 0.0 0.0
pair_coeff 1 1 0.07 3.55
pair_coeff 1 2 0.07 3.55
pair_coeff 2 2 0.07 3.55
bond_coeff 1 305.0 1.4
angle_coeff 1 40.000 120.00 35.00 2.41620
dihedral_coeff 1 3.100 2 180 0.0
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
timestep 2.0
# required for GPU acceleration
fix gpu all gpu force 0 0 1.0
# we only move some atoms.
group mobile type 1
# have balls bounce off the walls
fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
# take some potential energy out of the system
minimize 1.0e-4 1.0e-6 100 1000
reset_timestep 0
fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup.
fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only
compute mobtemp mobile temp
thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
thermo 1000
thermo_modify norm yes
thermo_modify temp mobtemp
run 100000000
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