I am trying to use Packmol to get an initial nanocomposite configuration for MD simulations. The problem is that I need to place the nanotube inside the PU chains and every time I try to rotate, the nanotube is always on the side of the PU chains (I need 100 chains) and never inside. Can you help me with some tips, please ?
my script:
tolerance 3.0
discale 1.5
seed 192911
filetype pdb
output nano_100_p.pdb
nloop0 1000
structure putube.pdb
number 100
inside box -140. -140. -160. 140. 140. 160.
end structure
structure nanotubo_solo_grande.pdb.pdb
number 1
inside cylinder 0. 0. -50. 0. 0. 50. 3. 100.
centerofmass
end structure
sidemax 10000