When setting up molecular simulations, choosing the right type of unit cell can significantly impact both the accuracy and performance of your calculations. Yet, many researchers default to cubic boxes out of convenience or familiarity—often without realizing the computational advantages of alternative geometries.
In SAMSON’s GROMACS Wizard, you can easily switch between several space-filling unit cell shapes. This affects how periodic boundary conditions (PBCs) are applied and can lead to noticeable reductions in simulation time, especially for systems like globular proteins or nanoscale particles surrounded by solvent.
The core idea: periodic boundary conditions
Periodic boundary conditions are often used in molecular dynamics to mimic an infinite system by repeating the simulation box in all directions. This helps to avoid artifacts from a system’s finite size. However, how you define the shape and size of this box—your unit cell—dictates how efficiently packing and interactions are calculated.
Why box shape matters
If your molecule is roughly spherical, using a cubic box wastes a lot of space. You end up simulating many unnecessary solvent molecules, which increases computational cost. Alternative geometries such as the rhombic dodecahedron or truncated octahedron more efficiently envelop spherical structures, reducing the number of solvent molecules needed to maintain the same minimum distance between periodic images.
Here’s a quick overview of the supported shapes in the GROMACS Wizard:
| Shape | Representation |
|---|---|
| Cubic |  |
| Orthorhombic |  |
| Triclinic |  |
| Rhombic dodecahedron |  |
| Truncated octahedron |  |
Why switch from a cube?
The rhombic dodecahedron is a particularly appealing option. For roughly spherical solutes, it reduces the simulation box volume to 71% of the volume of a cube with the same minimum image distance—saving about 29% CPU time. In practical terms, that could mean hours or even days less computation for long molecular dynamics runs.
How to choose in SAMSON
When preparing a system, you can pick the geometry that best suits your solute:
- Use the Prepare system step in the GROMACS Wizard.
- Select a desired unit cell type in the Choose unit cell section.
- Fine-tune dimensions by distance to the solute or explicit box lengths.
When used thoughtfully, this simple choice can lead to better-performing simulations without compromising on physical accuracy. For many researchers simulating biomolecules, this is one of the easiest ways to gain efficiency.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.