When setting up molecular dynamics simulations involving pulling—like center-of-mass (COM) pulling—it’s easy to overlook a crucial step: properly defining the simulation box. Yet, neglecting this may lead to artifacts caused by interactions with periodic images of the pulled molecule. If you’re pulling a structure within a periodic boundary condition (PBC) environment, box size isn’t just a detail—it’s a key part of building valid simulations.
Specifically, pulling simulations are constrained by the minimum image convention, which says that the pulling distance should be less than half the box length in the pulling direction. Otherwise, the pulled object may interact with its periodic image. Proper planning helps avoid unintentional forces that compromise results.
Setting Up the Box for COM Pulling
Let’s walk through an example scenario from the GROMACS Wizard tutorial: pulling chain A away from chain B by 5 nm in the z-direction.
Here’s how to define an appropriate box:
- Select an Orthorhombic box, which provides independent control over x, y, and z box lengths.
- Click the Compute fitted box option to initialize box dimensions based on the system.
- Then, manually override dimensions: set the box size to
6.5 nm x 4.5 nm x 12.0 nm. This ensures that 5 nm of pulling stays within half of the z-length (6 nm), complying with the minimum image convention while providing a safety buffer. - Offset the system slightly to ensure space in the pulling direction. Deactivate the “Center in box” option and set the center coordinates to
0.5 x 0.5 x 0.2.
This final step shifts the system toward the base of the box in the z-direction, granting enough room at the top for the pulling motion:
Why Proper Box Setup Matters
A too-small box risks atoms wrapping around and interfering with their own periodic images, skewing force results and potentially causing simulation failure. But an unnecessarily large box can also make your simulation less efficient thanks to additional solvent molecules and increased computation time.
By right-sizing your box—with consideration of pulling directions and distances—you both improve simulation accuracy and save time. For systems with diagonal or arbitrary pulling directions, SAMSON makes re-orienting easy via context menu options like Move selection > Align….
TIP: Visual Feedback Helps
The GROMACS Wizard in SAMSON provides a live visualization of your simulation box in the Viewport, so you can immediately see if box dimensions make sense with respect to the pulling motion. This immediate feedback can prevent dozens of wasted simulation runs due to unseen PBC issues.
Conclusion
Setting the simulation box isn’t just a preparatory step—it’s a critical design decision. When pulling molecules in simulations, take time to calculate box dimensions relative to pulling distance and direction. A correctly defined periodic box ensures validity and reproducibility of your results, while saving time in the long run.
To dive into the full tutorial, including system loading, minimization, and COM pulling simulations, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.