When setting up molecular dynamics simulations, especially with approximately spherical molecules in solution, most modelers focus heavily on force fields and solvent types. Yet, there’s an often-overlooked choice that can bring significant performance benefits: the shape of the unit cell used in the periodic boundary conditions.
If you’re using the GROMACS Wizard in SAMSON, you might have noticed multiple options for unit cell shapes: Cubic, Orthorhombic, Triclinic, Rhombic Dodecahedron, and Truncated Octahedron. These aren’t just geometric curiosities. Selecting the right shape can have a real impact on simulation efficiency.
For example, when simulating a roughly spherical solute, such as a globular protein, cubic boxes are commonly used — but not always optimal. In these cases, you can benefit greatly by choosing a more space-efficient unit cell shape that better wraps around the solute. This is where the Rhombic Dodecahedron and Truncated Octahedron come into play.
These unit cells approximate a sphere more closely than a cube does. Why does this matter? Because it takes fewer solvent molecules to fill the box around your solute while still maintaining a safe buffer zone to satisfy the minimum image convention. This means your system has fewer atoms, and therefore, your simulations run faster.
In fact, using a rhombic dodecahedron instead of a cube with the same minimum image distance can reduce the volume of your simulation box by 29%. This translates directly to less time spent in computation — which is a big deal when you’re running multiple trajectories or long simulations.
Here’s a quick comparison of the supported unit cell shapes in SAMSON’s GROMACS Wizard:
| Unit Cell Shape | Description |
|---|---|
| Cubic | Simple to set up, but not volume-efficient for spherical solutes. |
| Rhombic Dodecahedron | The most space-efficient; ideal for spherical systems. |
| Truncated Octahedron | Also space-saving and sphere-like, slightly larger than rhombic dodecahedron. |
You can choose your unit cell shape during the preparation step in the GROMACS Wizard interface. Use the visual options to fit the box to your system and select one that minimizes wasted space while respecting physical simulation constraints.
Ultimately, this small but impactful choice can help you optimize computational resources — especially important in batch projects involving many frames or conformations.
To learn more about unit cells and periodic boundaries in GROMACS Wizard, visit the original documentation page:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/periodic-boundary-conditions/
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