Manually Build Carbon Nanotubes in SAMSON with Pattern Editors

Carbon nanotubes (CNTs) are widely used in nanotechnology, materials science, and molecular simulation. But for many molecular modelers, designing a CNT manually—with precise atomic control—can be tedious and unintuitive. Whether you’re prototyping a custom topology or studying interactions at the atomic level, having to write scripts or use rigid templates limits creativity and precision.

SAMSON’s Pattern Editors provide a visual and interactive way to build carbon nanotubes from scratch using easily understandable manipulations. In this post, we’ll walk through a fully manual method for constructing a carbon nanotube using the Circular and Linear Pattern Editors in SAMSON, as described in the latest documentation.

Why Build CNTs Manually?

There are excellent generators for carbon nanotubes, including SAMSON’s own Carbon Nanotube Editor. However, manual control is useful when you’re:

  • Creating atypical or distorted nanotubes for simulations
  • Understanding how atomic arrangement affects electronic properties
  • Teaching nanoscale geometry with precise structural manipulation

Step-by-Step Guide: Building a Carbon Nanotube from Rings

  1. Create a ring structure: Start by building a planar carbon ring (e.g., benzene-like). Remove hydrogen atoms for clean edge bonding. You can rotate the ring to align its edge for pattern replication.
  2. Activate the Circular Pattern Editor (W): Use this tool to replicate the ring into a closed carbon loop. Set the number of instances (e.g., 12) and adjust the radius so that the ring ends align for bonding.
  3. Accept the circular pattern: This forms a fused carbon ring structure. Nearby atoms will merge automatically based on your preference settings.
  4. Align the ring in 3D space: Use the Edit > Align tool to place the ring in the XY plane to ensure that stacking builds along the Z-axis.
  5. Stack rings using the Linear Pattern Editor (L): Apply the linear pattern to replicate the ring along the Z-axis. For example, translate by 2 Å between rings and adjust rotation slightly if needed for chirality or bond alignment.
  6. Accept to finalize: This creates a tube-like structure. You now have a manually constructed carbon nanotube with full control over twist, spacing, and atom fusion.
  7. Minimize the geometry: After patterning, use the minimization tool to relax bond lengths and optionally re-add hydrogen atoms to clean up boundaries.

Interactive Controls Make It Easier

Each Pattern Editor lets you position, rotate, and duplicate structures using draggable widgets and numeric input. You can:

  • Scroll over the central widget to increase or decrease the number of replicas
  • Use Ctrl or Cmd + Scroll for fine control
  • Click the widget center to enter exact rotation angles and displacement values

This approach offers atomic precision without writing a single line of code.

Visual Preview

Interactive tutorial in SAMSON

Wrap-Up

Building carbon nanotubes manually in SAMSON is straightforward and gives you complete control over geometry and topology. Whether you’re crafting test systems or visualizing atomic arrangements, this technique is a great way to deepen your understanding of nanoscale design.

For more details, refer to the official documentation on Pattern Creation in SAMSON.

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

Comments are closed.