When preparing molecular simulations with periodic boundary conditions, one common challenge is selecting the most appropriate unit cell shape. This choice can impact your simulation’s efficiency and accuracy, especially when dealing with spherical or flexible biomolecules in solution. If you’ve ever wondered how to pick between cubic, triclinic, or more exotic cells like the rhombic dodecahedron, this post is for you.
The GROMACS Wizard in SAMSON offers five space-filling unit cell options:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
Each shape has its own geometric characteristics, but if you’re working with a macromolecule that roughly resembles a sphere (such as a folded protein in solvent), choosing the right shape can reduce solvent usage and save computational time. Here’s how they compare visually:
Why Go Beyond the Cube?
The rhombic dodecahedron and truncated octahedron are particularly efficient for spherical systems. Consider this: to maintain a minimum image distance (the shortest distance between a molecule and any of its periodic images), a cubic unit cell would need more volume than these two more spherical shapes.
For instance, the rhombic dodecahedron occupies only 71% of a cubic volume for the same periodic image distance. This translates to around 29% fewer solvent molecules and a similar reduction in required computation. Especially in solvent-heavy biomolecular simulations, that’s a direct savings of CPU time and memory.
How Do You Choose One in Practice?
In SAMSON’s GROMACS Wizard, you can select the unit cell shape and size during system preparation. Two fitting options are available depending on your setup:
- Box lengths: Specify the box dimensions directly. Ideal if you want a fixed box size across a conformational ensemble, such as a batch simulation.
- Solute-box distance: Specify a distance between the solute and the edges of the unit cell. A value of at least 1.0 nm ensures the minimum image convention is respected. This is especially useful when conformations vary in size.
Note: Although GROMACS always stores trajectories in a brick-like (rectangular) shape, SAMSON can auto-detect the unit cell type when you load simulation results. You can also adjust it manually in the trajectory importer dialog.
Bottom Line
If your system is roughly spherical or highly flexible, consider using a rhombic dodecahedron or truncated octahedron. You’ll reduce the required solvent, increase simulation efficiency, and still accurately reproduce the relevant physical interactions. If you’re unfamiliar with these cells, don’t worry—the GROMACS Wizard handles the heavy lifting and provides clear visual feedback during the setup process.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/periodic-boundary-conditions/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.