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

read_data cnt_6620.data
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

cnt_6620.data (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.