LAMMPS (21 Aug 2012)
# Tethered nanorods

atom_style	molecular

read_data	data.rigid.tnr
  1 = max bonds/atom
  orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
  1 by 1 by 1 MPI processor grid
  5600 atoms
  1600 bonds
  2 = max # of 1-2 neighbors
  1 = max # of 1-3 neighbors
  1 = max # of 1-4 neighbors
  2 = max # of special neighbors

# Specify bond parameters

bond_style	fene
bond_coeff	1 30.0 1.5 1.0 1.0

special_bonds	fene
  2 = max # of 1-2 neighbors
  2 = max # of special neighbors

# Specify initial velocities

velocity	all create 1.4 109345

# Specify rigid components

group		rods type 2	
4000 atoms in group rods
group		tethers	subtract all rods
1600 atoms in group tethers

neigh_modify 	exclude	molecule rods delay 0 every 1

# Specify the pair potentials

pair_style	lj/cut	2.5
pair_modify	shift	yes
pair_coeff	* * 1.0	1.0 1.122
pair_coeff	2 2 1.0 1.0 2.5

# Specify output

thermo	100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn

timestep	0.005

log		log.tnr