When setting up molecular dynamics simulations, especially using GROMACS, researchers often face a surprisingly impactful decision: what shape should the simulation box be? Choosing the right periodic unit cell shape can significantly reduce computational costs and resource usage, especially when simulating large or spherical solutes in a solvent. 🧪
The GROMACS Wizard in SAMSON supports several space-filling unit cell shapes. While a cube is the default choice many users stick with, it’s not always the best one. Shapes like the rhombic dodecahedron and the truncated octahedron can be much more efficient for simulating approximately spherical molecules like proteins. Why? Because those geometries are closer to a sphere than a cube is, meaning you need fewer solvent molecules to surround the solute while preserving physical accuracy.
Let’s take a closer look at your options:
| Unit cell shape | Representation |
|---|---|
| Cubic |  |
| Rhombic dodecahedron |  |
| Truncated octahedron |  |
Among these, the rhombic dodecahedron is particularly attractive: it fills space efficiently and its volume is only 71% that of a cube with the same minimum image distance. Put simply, when simulating a spherical molecule, this can lead to up to a 29% reduction in CPU time. That’s a lot of saved resources — especially when running long or batch simulations.
In SAMSON’s GROMACS Wizard, you can easily choose one of these shapes during system preparation:
Tips when choosing a unit cell:
- For roughly spherical macromolecules (e.g. globular proteins), prefer rhombic dodecahedron or truncated octahedron.
- Ensure at least 1.0 nm of space between the solute and the boundary to satisfy the minimum image convention.
- The total system volume impacts not just RAM but also the number of particles simulated — this affects runtime and thermal properties.
While GROMACS keeps particles within a brick shape internally, SAMSON will recognize and adapt to your selected unit cell shape, letting you visualize systems more naturally in 3D — and even adjust them in the importer when needed.
Learn more in the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.