<< Using a cylinder region from a nanotube >>

[icamps]

Hi, I want to add some CO molecules around a boron-nitride nanotube. The steps I followed:

• Calculate the centroid of several atoms in the base face of the nanotube and use the coordinates as a1, b1, and c1.
• Calculate the centroid of several atoms in the top face of the nanotube and use the coordinates as a2, b2, and c2.
• Measure the radii of the nanotube and use it as d.
• Measure the length of the nanotube and used it as l.
• (all measurements are in Ångströms)

The final structure I got, the CO molecules are distributed too far around the nanotube in such a way that when loaded in Jmol, the nanotube is just a little point in the middle of the screen and the CO molecules are too way small too.

The input and output files are attached.

What I am doing wrong?

Thanks in advance.

Camps nanotube.zip

[basillicus]

Hi,

you are missing the maximum boundaries where to put the molecules in. The CO molecules are added outside the cylinder, but they have no maximum limit where they may be allocated. Hence, the molecules, without that constraint are really far apart. Adding the inside box in your CO structure should solve the problem.

Try this

filetype pdb
tolerance 2.0
output test.pdb
seed -1

# Load the Boron Nitride Nanotube structure and keep it fixed, with no translation nor rotations
structure BNH.pdb
  fixed 0. 0. 0. 0. 0. 0.
end structure

# Load number of molecules, outside the cylinder (nanotube) AND WITHIN a bounding box
structure CO.pdb
  number 30
  outside cylinder 0. 0. 0. 0. 0. 1. 3.92 17.31
  inside box 0. 0. 0. 18. 18. 17.31
end structure

[icamps]

Hi @basillicus , thanks for your help, it worked like a charm.

[lmiq]

Thank you both for the feedback and help. I've been out of work for some time because of a newborn at home.

[basillicus]

@lmiq Such a fantastic news! Congratulations!

@icamps , glad it worked!