When setting up molecular dynamics simulations, one of the often overlooked decisions is the choice of the unit cell shape used for periodic boundary conditions. Yet, this decision can have a significant impact on simulation efficiency and accuracy—especially when dealing with macromolecules in solution.
If you’ve been selecting the default cubic box without much thought, it’s worth taking a closer look at how different shapes affect your results and computational cost. Let’s explore the unit cell options available in the GROMACS Wizard for SAMSON, and when to use them.
Available Unit Cell Shapes
The GROMACS Wizard provides five space-filling unit cell geometries:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic Dodecahedron
- Truncated Octahedron
Understanding the Trade-Offs
While the cubic box is simple and commonly used, it’s not always efficient for spherical or flexible macromolecules like proteins. That’s where shapes like the rhombic dodecahedron or truncated octahedron come in.
These two shapes are closer to being spherical, which means they can enclose a spherical object with less empty space. This has several advantages:
- Reduced number of solvent molecules: Less space to fill means fewer water molecules, saving memory.
- Faster simulations: Fewer particles = fewer calculations = lower CPU time.
In fact, the rhombic dodecahedron uses only 71% of the volume of an equivalent cubic box. That translates to a potential CPU time saving of around 29% for roughly spherical solutes.
When Should You Use Which?
If your system is close to spherical (e.g. a globular protein or a micelle), it’s highly recommended to use either the rhombic dodecahedron or the truncated octahedron. Both are supported in SAMSON’s GROMACS Wizard when preparing a system.
The choice can be made during the preparation step simply by selecting the desired unit cell shape. You’ll find the option in the system preparation interface, where you can also modify the box size or solute-box distance based on your needs.
A Note on Reproducibility
For batch simulations, you might want consistent box sizes across all frames or conformations. In this case, explicitly setting the box lengths is a good approach. Alternatively, if your system changes shape during the trajectory (e.g. a protein folding pathway), choosing solute-box distance will adapt the box per frame to maintain valid periodic boundary conditions.
Conclusion
Choosing the right unit cell shape is a simple yet impactful step in setting up your simulation. For spherical or flexible solutes, switching from a cubic box to a rhombic dodecahedron or truncated octahedron can save computational resources while maintaining accuracy. It’s one of those optimizations that many overlook, but the performance gains—especially at scale—can be significant.
Explore your options directly in the GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.