How to Build a Carbon Nanotube Step-by-Step in SAMSON

Designing accurate nanoscale structures is a challenge many molecular modelers face, especially when trying to create periodic or symmetric systems like carbon nanotubes. Manually duplicating and arranging atoms to form a 3D tube with precise geometry can be both time-consuming and error-prone.

Fortunately, SAMSON offers a powerful yet intuitive solution using its Pattern Editors. In this post, we’ll walk through how to build a carbon nanotube manually using SAMSON’s Circular and Linear Pattern Editors, providing control over atomic arrangement and symmetry across 3D space.

Why build it yourself?

While SAMSON includes a dedicated Carbon Nanotube Editor, constructing one manually is a great way to learn how Pattern Editors work. It also gives you full control over geometry, especially if you’re designing non-standard tubular structures or modifying existing ring systems.

Step-by-step: Constructing a Carbon Nanotube

  1. Create a ring molecule: Begin by building a basic carbon ring in SAMSON (e.g., a benzene-like ring). Remove any hydrogen atoms and rotate it so that the carbon edges align horizontally in the viewport.
  2. Apply the Circular Pattern Editor (shortcut: W):
    • Use the widget to increase the number of copies (e.g., 12) to form a full ring.
    • Adjust the radius interactively or enter a precise value to ensure bonding distances match expected carbon-carbon bonds.
    • Click Accept to merge overlapping atoms and create a symmetrical base ring.
  3. Align the ring to the XY plane: Use the Align tool (Edit > Align) to position the ring properly in 3D space. This helps when stacking multiple rings to form the tube.
  4. Duplicate along Z-axis with the Linear Pattern Editor (shortcut: L):
    • Change the translation settings (e.g., 2 Å along Z-axis) so each ring sits above the previous one without overlapping.
    • If required, add a small rotational increment to mimic helical symmetry.
    • Adjust the copy count using mouse scroll or hold Ctrl / Cmd + scroll for quicker changes.
    • Click Accept to finalize the nanotube structure.
  5. Finalize the structure: Run energy minimization on the nanotube to correct any small distortions and optionally add hydrogen atoms at the tube ends if needed.

This method empowers you to build custom nanotubes, including those with functionalized ends or altered geometries for simulations in materials science, nanomedicine, or biomolecular research.

Visual example from an interactive tutorial

Interactive tutorial in SAMSON

To learn more about pattern editors and nanotube design, visit the full documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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