If you’ve ever set up a molecular dynamics simulation, chances are you’ve spent time choosing the right periodic boundary conditions. But one decision that often gets overlooked — and can significantly affect simulation efficiency — is the shape of the unit cell. Choosing the right shape can help reduce solvent use and speed up computations, sometimes by almost a third. Let’s look at how GROMACS Wizard in SAMSON helps you pick the best cell for your system.
Why unit cell shape matters
When studying structures like spherical macromolecules (for example, proteins in solution), the cubic box might not be the most efficient shape. Cubes are easy to work with, but they leave empty volume at the corners, requiring extra solvent molecules. To simulate the same system, a better-fitting shape could significantly reduce the number of atoms you need to calculate — and that means shorter simulation times and better use of compute resources.
Visual guide to cell shapes
In GROMACS Wizard, multiple space-filling shapes are available when you define your periodic box:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
Benefits of compact unit cells
If your system resembles a sphere or a roughly globular shape, the following two options may save considerable simulation time:
- Rhombic dodecahedron: This is the most compact and regular space-filling unit cell. With only 71% of the volume of a cube with the same image distance, you reduce the number of solvent molecules needed — potentially cutting down 29% of CPU use.
- Truncated octahedron: Also closer to a sphere than a cube, which makes it another efficient choice for solvent boxes around globular proteins.
These options can be selected directly in the system preparation step:
How to choose
Picking the right unit cell depends on two main factors:
- Shape of your solute: Is your molecule fairly spherical or elongated? Compact shapes benefit most from rhombic dodecahedra and truncated octahedra.
- Minimum image convention: Always ensure that no molecule interacts with its own periodic image. This typically means keeping at least 1.0 nm between solute and box boundary. GROMACS Wizard offers two fitting modes:
- Box lengths: Set exact dimensions if you want one consistent box shape for all conformations.
- Solute-box distance: Automatically adjust the box around your structure with a chosen buffer distance.
Automatic detection during import
Useful tip: when loading GROMACS results, SAMSON tries to automatically detect your unit cell. However, you can still update it manually in the import dialog if needed.
Choosing the right unit cell shape can significantly reduce simulation time and resource use — and GROMACS Wizard makes it easy to apply best practices for molecular modeling setups.
Learn more about periodic boundary conditions in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.