When setting up molecular simulations, one challenge that modelers often face is finding the right balance between accuracy and computational efficiency. Many simulation tasks—especially when working with spherical or flexible macromolecules like proteins—require significant solvent padding to respect periodic boundary conditions. But the shape of the unit cell can make a surprising difference.
The GROMACS Wizard in SAMSON lets you select from several unit cell shapes when preparing your simulation: Cubic, Orthorhombic, Triclinic, Rhombic Dodecahedron, or Truncated Octahedron. Each of these shapes fills space in a different way, which may directly impact how many water molecules—or other solvents—you need to add before your system is ready to go.
Why Does Unit Cell Shape Matter?
A cube might seem like the easiest and most intuitive shape to use, but it’s not necessarily the most efficient. If you’re modeling a near-spherical system, the cubic box results in a lot of wasted volume—because you’re forced to fill solvent in the corners that your macromolecule will never reach.
Shapes like the rhombic dodecahedron and truncated octahedron do a better job minimizing this excess volume while still maintaining periodicity. In fact, the rhombic dodecahedron can reduce the required solvent volume by up to 29% compared to a cube of the same image distance. That implies nearly a third less computation time in water-heavy systems—an efficient option that’s often overlooked.
Which One Should You Pick?
Here’s a quick comparison of the common unit cell shapes SAMSON supports via the GROMACS Wizard:
| Unit Cell Shape | Description |
|---|---|
| Cubic | Simple and intuitive, but inefficient for spherical systems. |
| Orthorhombic | Useful for elongated molecules. Not optimal for spheres. |
| Triclinic | General-purpose, accommodates any angles between vectors. |
| Rhombic dodecahedron | Efficient for spherical molecules; minimizes solvent volume. |
| Truncated octahedron | Also good for spheres; more regular than a cube. |
How to Choose the Unit Cell in SAMSON
The GROMACS Wizard in SAMSON offers an intuitive interface for selecting your unit cell and system fitting strategy:
You can choose to:
- Manually set box lengths and adjust its dimensions.
- Specify solute-box distance, which pads the system based on your defined spacing (typically 1.0 nm, to respect the minimum image convention).
Remember: GROMACS always keeps particles in a brick-shaped volume internally. SAMSON will attempt to detect the original unit cell when loading your trajectory to help with consistency.
Conclusion
Choosing the right unit cell shape isn’t just about aesthetics—it’s a way to significantly reduce computational resources and simulation times. If you frequently work with roughly spherical biomolecules, consider giving the rhombic dodecahedron or truncated octahedron a try in your next system prep.
Click here to learn more about unit cell shapes and periodic boundary settings in the GROMACS Wizard for SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.