When setting up molecular dynamics simulations with periodic boundary conditions in GROMACS, a common challenge is: how to choose the right simulation box shape. Many users default to cubic cells, but there are smarter options available — especially if you’re working with approximately spherical macromolecules like proteins.
Why does this matter? The shape of your unit cell has a direct impact on simulation efficiency. A poorly chosen unit cell can lead to the inclusion of unnecessary solvent molecules, increasing memory usage and CPU time. That’s where SAMSON’s GROMACS Wizard offers a helpful solution with built-in support for various space-filling unit cell shapes.
What Unit Cell Shapes Can You Use?
The GROMACS Wizard supports:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
Let’s focus on the rhombic dodecahedron and the truncated octahedron. These two shapes stand out for systems where the macromolecule is approximately spherical. Why? Because they’re closer to being a sphere than a cube is — meaning you can surround your molecule with fewer solvent atoms for the same buffer distance to its periodic image.
The rhombic dodecahedron is the most compact of the space-filling options. Compared to a cube with the same minimum image distance, its volume is only 71%. That’s a potential CPU time savings of almost 29% when simulating solvated biomolecules. In other words, smaller box, fewer atoms, less compute time.
How to Set It Up in SAMSON
When using the GROMACS Wizard in SAMSON, you can choose your desired unit cell during the preparation stage. Two fitting methods are available:
- Box lengths: You define the box size directly. It fits tightly to your system, but you should increase the size manually to satisfy the minimum image convention.
- Solute-box distance: You specify a thickness of the solvent layer around your system. This is the simpler option and ensures you don’t accidentally shrink-wrap your molecule.
Tip: At least 1.0 nm between your solute and the box wall is recommended as a rule of thumb.
If you’re importing GROMACS results into SAMSON, it will try to auto-detect the unit cell shape. You can still adjust it manually in the Importer dialog if needed.
Why It’s Worth the Extra Click
Even small efficiency gains per simulation can quickly add up, especially if you’re dealing with batches of trajectories or replica simulations. By choosing a compact unit cell like a rhombic dodecahedron, you can:
- Create smaller systems (faster to simulate)
- Maintain the same accuracy
- Use resources more efficiently
Having these advanced options integrated directly into GROMACS Wizard makes them more accessible — especially for those who prefer visual toolsets over command-line setup.
📘 Learn more in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use.
You can download SAMSON at https://www.samson-connect.net.