When setting up molecular dynamics simulations with periodic boundary conditions in GROMACS, one of the first steps is defining the unit cell shape. This decision directly affects the computational efficiency of your simulation and how well it reflects your system’s geometry.
Fortunately, if you’re using the GROMACS Wizard in SAMSON, you have access to several space-filling unit cell shapes, each with their own characteristics. Understanding the implications of each shape can help reduce simulation cost and prevent artifacts due to inappropriate box dimensions.
Available Unit Cell Shapes
The GROMACS Wizard supports the following unit cell shapes:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
All of these shapes are compatible with periodic boundary conditions. However, choosing between them depends on the shape of your molecular system. If your system is roughly spherical (e.g., a globular protein), using a rhombic dodecahedron or a truncated octahedron instead of a cube can significantly improve performance by reducing the number of solvent molecules needed to fill the box.
Why Shape Matters
The goal in choosing a unit cell shape is to minimize the simulation volume while maintaining sufficient distance between periodic images of your solute. This ensures that non-bonded interactions aren’t calculated between mirrored copies of the same molecule, which would violate the minimum image convention.
Here’s why the choice matters:
- A cube is simple but often inefficient for non-cubic molecules.
- Rhombic dodecahedron and truncated octahedron offer better volume efficiency for spherical solutes. The rhombic dodecahedron, in particular, has only 71% the volume of a cube with the same image distance—this leads to up to a 29% reduction in the number of solvent molecules and CPU time.
| Unit Cell Shape | Image |
|---|---|
| Cubic |  |
| Orthorhombic |  |
| Triclinic |  |
| Rhombic dodecahedron |  |
| Truncated octahedron |  |
When Should You Use Non-Cubic Boxes?
If you’re simulating a spherical or flexible biomolecule in solution, you’ll likely benefit from using either a rhombic dodecahedron or a truncated octahedron. These reduce the box volume without compromising the minimum distance between solute images.
The reduction in box volume:
- Saves memory and disk space
- Speeds up simulations by reducing the number of solvent molecules
- Preserves solvation quality for approximately spherical systems
The GROMACS Wizard lets you interactively choose a unit cell shape and fine-tune your system’s box size through either direct box length input or specifying a solute-box distance (with at least 1 nm recommended).
Conclusion
Optimizing unit cell shapes may seem detail-oriented, but the gains in simulation efficiency and accuracy are worth the attention. By matching the unit cell geometry to your solute’s shape, especially when dealing with spherical biomolecules, you can avoid unnecessary overhead and simulation artifacts.
To learn more about unit cell design and periodic boundary conditions in GROMACS Wizard, visit 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.