Periodic boundary conditions are fundamental for molecular dynamics simulations. They let us simulate a small region of a much larger system, avoiding edge effects. But here’s something that often gets overlooked: the shape of the unit cell you choose matters—a lot. If you’re modeling roughly spherical molecules (think typical proteins or flexible polymers), using a cubic box might actually be wasting your valuable computational resources.
In SAMSON’s GROMACS Wizard, you can easily switch between different unit cell shapes to optimise your simulation setup. While the cubic cell is the default and well-known, alternative geometries like the rhombic dodecahedron or truncated octahedron can reduce the number of solvent molecules needed to fill your box. That results in fewer particles and, consequently, faster simulations.
Why shape matters
Let’s say you’re simulating an approximately spherical macromolecule, like a globular protein. If you use a cubic unit cell to ensure the minimum image convention (i.e., the solute doesn’t interact with its own periodic images), you’ll need a lot of solvent to fill the box, leading to more atoms and longer simulation times.
Enter the rhombic dodecahedron and truncated octahedron unit cells. These shapes are more compact around a spherical solute. In fact, a rhombic dodecahedron box has only 71% of the volume of a comparable cubic box. That potentially means around 29% less computation time per simulation—which adds up quickly.
Visual guide to available shapes
Here’s a quick overview of the box shapes supported by SAMSON’s GROMACS Wizard:
- Cubic: Common default shape; simple but inefficient for spherical solutes.
- Orthorhombic: Like a stretched cube; still inefficient for spheres.
- Triclinic: Fully general unit cell; often used for complex lattice systems.
- Rhombic dodecahedron: Great for spherical molecules; reduces solvent and computation time.
- Truncated octahedron: Also efficient for round systems, though a bit more complex.
Each of these options can be selected during the system preparation step in SAMSON:
When to use which
So when should you switch to a rhombic dodecahedron or truncated octahedron?
- If your solute is roughly spherical.
- If you want to reduce the number of water molecules / solvent.
- If you’re running simulations on limited computing resources or for long periods.
A word of caution: GROMACS stores trajectories in a brick-shaped volume for performance reasons, but SAMSON can automatically detect and interpret the correct unit cell shape when loading them. You can also manually adjust this via the importer settings.
Optimizing your unit cell shape is a small change with potentially big impact. If you ever found your simulation annoyingly slow and you were using a cubic box—this might be the low-hanging fruit you didn’t know you had.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.