Working on a molecular simulation in solution? If the system you’re modeling is approximately spherical—like a protein, micelle, or nanoparticle—you might be wasting compute time without realizing it. Let’s talk about unit cell shapes and how your choice impacts performance and accuracy in simulations using periodic boundary conditions.
When you simulate a molecular system with periodic boundary conditions, the space you’re simulating is essentially tiled with copies of your system. You define a unit cell that fills space, and that cell repeats in all directions. The shape of that cell affects how much solvent you need and, as a result, how much computational power you use.
What Shapes Are Available?
The GROMACS Wizard in SAMSON supports several shapes for space-filling unit cells:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
Each shape has different space-filling properties. The cube is simple but inefficient for spherical solutes. Enter the rhombic dodecahedron and the truncated octahedron.
Smaller Volumes, Less Solvent
Why do these two shapes matter?
Both the rhombic dodecahedron and truncated octahedron are closer to spheres than cubes are. This means they can enclose your solute more efficiently, reducing the volume that needs to be filled with solvent—and that means less CPU time and memory consumption.
For example:
- The rhombic dodecahedron requires only 71% of the volume of an equivalent cube with the same minimum image distance.
- This leads to a potential 29% savings in CPU time during simulations of spherical or flexible molecules in solvent.
When you prepare your system in the GROMACS Wizard, you can choose the unit cell shape along with its size. This happens during the system preparation stage.
How to Choose?
If your molecule is roughly spherical or flexible, and you’re simulating it in solution, consider using the rhombic dodecahedron or truncated octahedron. You’ll maintain the same level of physical accuracy while optimizing resource usage.
Also, think about how you define your box:
- Box lengths: define the size explicitly and tightly fit it around your system; useful for batch simulations.
- Solute-box distance: define the distance between solute and box edges (at least 1 nm recommended to ensure the minimum image convention); more flexible option per frame or conformation.
Final Tip
GROMACS always stores data in a rectangular (brick-shaped) layout for performance reasons. When loading results into SAMSON, it automatically tries to detect the originally used unit cell. But you always have the option to change it at import if needed.
Choosing the right box shape can save time, reduce resource usage, and help you get results faster—without compromising on scientific rigor.
To learn more, visit the full documentation page on periodic boundary conditions.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.