When setting up molecular dynamics (MD) simulations using GROMACS, one decision often overlooked—but critically important—is the choice of the unit cell shape used in periodic boundary conditions (PBCs). The shape of your simulation box directly impacts resource usage and simulation efficiency, especially when working with solvated macromolecules such as proteins or nanoparticles.
SAMSON’s GROMACS Wizard simplifies this choice by allowing you to define the unit cell shape and size during system preparation. But how do you choose the right one?
Why the Unit Cell Shape Matters
In molecular simulations, we use periodic boundary conditions to simulate an infinite system by replicating the simulation box in all directions. However, a poorly chosen unit cell may significantly increase the number of solvent molecules required to fill the box—or worse, result in inaccuracies due to interactions with a molecule’s own periodic image.
Supported Unit Cell Shapes
The GROMACS Wizard in SAMSON supports five unit cell shapes:
| Unit Cell Shape | Image |
|---|---|
| Cubic |  |
| Orthorhombic |  |
| Triclinic |  |
| Rhombic Dodecahedron |  |
| Truncated Octahedron |  |
Recommendations Based on Molecular Shape
- Spherical or flexible macromolecules (e.g., proteins, DNA): Use rhombic dodecahedron or truncated octahedron. These shapes are more space-efficient than a cube and can reduce the number of solvent molecules needed. For example, a rhombic dodecahedron has only 71% the volume of a cube with the same periodic image distance—saving about 29% in CPU time.
- Rectangular or elongated systems: Stick with a cubic or orthorhombic box. Their uniform geometry is easier to handle for systems with aligned constraints or directional forces.
- Crystal structures or non-90°-angled lattice vectors: Use a triclinic box to match your crystal symmetry.
Adjusting Unit Cell Size
The GROMACS Wizard gives you two options to define how the system fits within the chosen box shape:
- Box lengths: Specify exact box dimensions. Ideal when you need consistent box sizes across multiple conformations.
- Solute-box distance: Specify the minimum distance between solute and box edge. Recommended to be at least 1.0 nm to avoid solute interacting with its own periodic image. This ensures the minimum image convention is satisfied.
When preparing batch projects, using the solute-box distance method means the box size will adapt to each frame—handy when simulating a dynamic pathway or multiple conformers of a molecule.
Final Thoughts
Choosing the right unit cell shape doesn’t have to be guesswork. By considering the geometry of your system and understanding the trade-offs, you can significantly reduce computational cost and avoid unintended artifacts. Small choices at setup can have big impacts on simulation fidelity and performance.
To learn more, refer to the full SAMSON documentation page on Periodic Boundary Conditions.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.