CNT getting deformed at edges

Dear All,

I am doing a carbon nanotube (6,6 ) of 20 Angstrom simulation in NVT ensemble using Lammps.

I generated the lammps data file using topo tool in vmd and kept the box lengths as given by VMD.

However during minimization I find that the nanotube is getting compressed at the ends on both

ends in z direction. While the run script is given below the data file is also attached. I would be

highly obliged if some one can identify the abnormal deformation of CNT.

dimension 3
units real
boundary p p p

atom_style full
pair_style lj/cut 11.0
bond_style harmonic
angle_style harmonic
pair_modify mix arithmetic

group cnt type 1

set group cnt charge 0.00

neighbor 3.0 bin
neigh_modify delay 1

minimize 1.0e-4 1.0e-6 100 1000
#fix 1 wtr shake 0.0001 20 0 t 2 3 a 1 b 1
#fix 2 cnt setforce 0.0 0.0 0.0

fix 1 cnt nvt temp 300.0 300.0 100.0

fix 3 all momentum 50 angular

timestep 1.00

thermo 1000
thermo_style custom step pe ke etotal temp press vol

restart 50000 z.restart

dump 2 all custom 1000 cnt.lammpstrj id type x y z
#dump 3 all custom 1000 z2.output.dump id type fx fy fz

run 500000 (25.7 KB)

Is your CNT of finite length (roughly 20A) or infinite (periodic) along Z? If it is the former, then your box dimension along Z (21.61 A) is too small resulting in head-tail interaction across the periodic boundary. If it is the later, your box dimension is likely not correct. A periodic unitcell of (6,6) CNT has a length of ~2.46 A along Z, and 21.61 is not a integer multiple of 2.46.