When setting up molecular dynamics simulations, especially in solvents, minimizing computational cost while preserving accuracy is always top of mind. One crucial yet sometimes overlooked factor is the shape of the unit cell used when applying periodic boundary conditions (PBC).
By default, many molecular modelers opt for cubic boxes because they’re easy to visualize and simple to implement. However, this choice can be inefficient—when simulating approximately spherical biomolecules like proteins or nucleic acid complexes, a cubic box often includes far more solvent than necessary. This means longer simulation times and increased resource usage without added benefit.
The GROMACS Wizard in SAMSON offers a simple way to explore various unit cell geometries that might be more appropriate, depending on your system:
| Unit Cell Shape | Visualization |
|---|---|
| Cubic |  |
| Truncated Octahedron |  |
| Rhombic Dodecahedron |  |
Both the rhombic dodecahedron and the truncated octahedron are more space-efficient than cubes. For example, the rhombic dodecahedron has only about 71% of the volume of the cube for the same minimum distance between periodic images. That means up to 29% fewer solvent molecules and a similar reduction in computational time when simulating spherical or flexible molecules.
When using the GROMACS Wizard, you can choose your unit cell shape and simulate more efficiently by selecting:
- Box lengths – tightly fit the system and adjust manually to satisfy the minimum image convention.
- Solute-box distance – automatically add a recommended buffer (usually ≥ 1 nm) around the molecule.
Important: even though these unit cells are tighter, GROMACS internally represents the systems in brick-shaped volumes for efficiency. When importing simulation trajectories, SAMSON tries to detect and match the correct unit cell automatically, but you can override the type as needed.
Switching away from default cubic boxes may not seem like a big deal, but over the course of thousands of simulations, selecting a more suitable unit cell can significantly speed up your work and reduce resource usage—without compromising on simulation accuracy.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.