When setting up a molecular dynamics simulation, choosing the right boundary conditions can significantly influence both accuracy and performance. One key, yet often overlooked, aspect is the shape of the unit cell used for periodic boundary conditions.
By default, many users opt for a cubic box. It’s familiar and straightforward. But when studying a roughly spherical molecule in solvent (like many proteins), a cubic box may not be the most efficient choice.
Different Shapes, Different Trade-Offs
The GROMACS Wizard in SAMSON offers a range of space-filling unit cell shapes:
- Cubic
- Orthorhombic
- Triclinic
- Rhombic dodecahedron
- Truncated octahedron
Among these, the rhombic dodecahedron and truncated octahedron stand out for spherical systems. Why? Because they are closer to the shape of a sphere, they need fewer solvent molecules to achieve the required spacing between periodic images. For example, a rhombic dodecahedron has only 71% the volume of a cube with the same image distance, reducing the solvent count and potentially saving up to 29% of CPU time.
This is especially useful when processing long trajectories or simulating flexible, solvated biomolecular systems. Not only do you save computational time, but you also reduce memory usage and disk space for storing solvent-heavy trajectory data.
Initial Box Fitting: Two Approaches
When setting up your system in SAMSON’s GROMACS Wizard, you can choose between two ways of defining the box:
- Box lengths: Directly specify the box size. This fits the box tightly to your solute, but be cautious — you’ll need to manually ensure that the solute does not interact with its periodic image.
- Solute-box distance: Specify the padding between the solute and the box wall. At least 1.0 nm is recommended to satisfy the minimum image convention.
For batch projects involving multiple conformations, these settings determine whether the same box is applied to all frames (Box lengths) or whether it adapts per frame (Solute-box distance).
Isn’t It Always a Box?
Behind the scenes, GROMACS always stores data as if the box is a brick for efficiency. But SAMSON’s GROMACS Wizard interprets this correctly upon loading trajectories and lets you visually and computationally work with the actual unit cell shape you selected.
So the next time you prepare a spherical system, consider skipping the cube and try a rhombic dodecahedron or a truncated octahedron instead. It could make your simulations faster without sacrificing accuracy.
To explore more about unit cells and periodic boundary conditions, visit the full documentation page: GROMACS Wizard – Periodic Boundary Conditions.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.