Building Carbon Nanotubes by Hand in SAMSON

Carbon nanotubes (CNTs) are remarkable structures used in nanotechnology, materials science, and even drug delivery. But building them manually in a molecular editor can be tedious and error-prone—especially when dealing with atomic-level precision and numerous repetitions.

In this post, we’ll walk through how to design a carbon nanotube manually using SAMSON’s Pattern Editors. This approach combines intuitive on-screen controls with precise transformations, offering a reproducible workflow without scripting. Whether you’re modeling nanotubes for simulation or visualization, this method saves clicks and ensures structural accuracy.

From a Ring to a Tube

To build a carbon nanotube, we begin with a ring of carbon atoms and then stack it vertically. Here’s how to do it:

  1. Create a ring of carbon atoms. You can use the atom building tools in SAMSON and remove hydrogen atoms afterward to leave a clean carbon framework.
  2. Orient the ring using SAMSON’s movement tools so that its plane lies in the XY plane (flat, facing upwards).
  3. Activate the Circular Pattern Editor (shortcut: W) to replicate the original ring tangentially:
    • Set the instance count (e.g., 12) to form a complete circle.
    • Adjust the radius so atoms at the edges are near each other—SAMSON will optionally merge overlapping atoms to form bonds.
  4. Finalize the ring pattern by clicking the Accept button.
  5. Align the resulting ring structure using Edit > Align to ensure it sits appropriately on the Z=0 plane.
  6. Switch to the Linear Pattern Editor (shortcut: L) to replicate the ring along the vertical (Z) axis:
    • Set a vertical translation step (e.g., 2 Å) between layers.
    • Optionally, rotate each layer incrementally if your tube design calls for helicity.
    • Use Ctrl + scroll to increase the number of instances quickly.
  7. Accept the result to finalize your carbon nanotube model.
  8. Minimize the structure to relax strained bonds and optionally add hydrogens at exposed sites.

Why This Helps

Manually building nanotube geometries in traditional modeling tools often involves many manual edits, repetitive positioning, and little visual feedback. SAMSON’s pattern-based approach introduces:

  • Interactive widgets for positioning and aligning molecules easily.
  • Precision input that allows accurate tuning of distance and rotation values.
  • Instant feedback to test and adjust geometries before committing.

The process is also useful when you’re exploring customized topologies—not just standard nanotube templates. For instance, you can experiment with chirality or apply curved patterns for more exotic tubular geometries.

Resources to Learn More

This example is covered in the SAMSON 2025 webinar, and you can follow the official documentation for further technical details. There’s also a built-in Carbon Nanotube Editor in SAMSON for even faster building, but building it manually gives you more geometric flexibility.

Interactive tutorial in SAMSON

Want to dive deeper? Explore the full documentation page here.

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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