in.bucky-plus-cnt
a920f2320475runner

in.bucky-plus-cnt
View Options

			# stick a buckyball into a nanotube
			units real
			dimension 3
			boundary f f f
			atom_style molecular
			newton on off

			processors * * 1

			# read topology
			read_data data.bucky-plus-cnt

			pair_style lj/cut 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 4.0 bin
			neigh_modify delay 0 every 1 check yes

			timestep 2.0

			# 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