When setting up molecular dynamics (MD) simulations, especially for biomolecules in solution, one of the often overlooked choices is the shape of the simulation unit cell. This decision directly impacts the number of solvent molecules needed, the volume to be simulated, and ultimately, the computational cost.
Fortunately, GROMACS Wizard in SAMSON offers several pre-configured unit cell shapes that you can select when preparing your system. Understanding these options, and when to choose one over another, can help streamline your simulations and optimize performance.
Why Unit Cell Shape Matters
Unit cells must fill space without gaps, and their geometry determines how periodic boundary conditions are applied. When simulating solutes (like proteins), you also want to maintain a minimum image distance to make sure atoms don’t interact with their own periodic images.
More spherical unit cells offer efficient packing around approximately globular molecules, requiring fewer solvent molecules to fill the box — which means faster simulations.
Space-Filling Unit Cell Options in GROMACS Wizard
SAMSON’s GROMACS Wizard supports the following unit cell shapes:
| Unit cell shape | Representation |
|---|---|
| Cubic |  |
| Orthorhombic |  |
| Triclinic |  |
| Rhombic dodecahedron |  |
| Truncated octahedron |  |
Which Shape Should You Use?
For spherical or flexible biomolecules in solution, such as globular proteins or peptides, the rhombic dodecahedron and the truncated octahedron are typically better choices than cubic boxes. These polyhedral shapes approximate spheres more closely, which means less space is wasted on solvent not directly surrounding the solute.
In practical terms, using a rhombic dodecahedron can reduce your simulation volume to ~71% of the volume of a cube with the same image distance — potentially saving around 29% of CPU time. That can translate into hours or even days saved across long or repeated simulations.
How to Choose in GROMACS Wizard
When preparing a system in SAMSON’s GROMACS Wizard, you can select your preferred unit cell under the Choose Unit Cell stage. An illustration provides a clear visual cue to confirm your choice:
If you’re running a simulation batch across several conformations or a trajectory path, you might prefer setting the Box lengths to keep the unit cell size uniform. Alternatively, the Solute-box distance parameter allows variable sizing between frames.
Conclusion
The shape of your unit cell could be the difference between waiting hours versus days for simulations to complete. If you’ve been using cubic boxes by default, it might be time to rethink that habit.
Learn more about unit cell shapes and boundary conditions in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.