When setting up molecular dynamics (MD) simulations with pulling forces—especially center-of-mass (COM) pulling—one common but potentially problematic decision is defining the simulation box size. Selecting inappropriate box dimensions can interfere with the pulling process and compromise the reliability of results.
In the GROMACS COM pulling tutorial using SAMSON‘s GROMACS Wizard Extension, defining the box is a critical preparatory step to avoid unexpected interaction artifacts caused by periodic boundary conditions.
Why Box Size Matters in Pulling Simulations
When a chain is pulled inside a periodic system, a too-small box can result in the pulled part “wrapping around” the box, interacting with itself or other components. This breaks the validity of the simulation due to violations of the minimum image convention, which assumes particles only interact with their closest periodic images.
Setting the Box Size in SAMSON
In this workflow, the molecule 2BEG is used, and the pulling is done along the z-direction. The key is to plan ample space in the pulling direction. Since we pull chain A away from chain B by 5 nm, the box should be at least twice this distance plus a buffer.
Recommended Settings:
- Use an Orthorhombic box
- Box dimensions:
6.5 nm × 4.5 nm × 12 nm - Deactivate Center in box option
- Set center to
0.5 × 0.5 × 0.2
This configuration ensures at least 6 nm of space above and below the pulling direction’s starting point—well above the 5 nm required, and more than enough to avoid periodic artifacts.
Visual Confirmation Helps
When the box is correctly defined, it’s visualized directly in the Viewport within SAMSON. This immediately shows how much room is available in the pulling direction, letting you double-check that the setup is safe before launching long simulations.
Bonus Tip: Align the Pulling Direction
If your pulling vector is not naturally aligned with one of the coordinate axes, SAMSON lets you reorient the system using Move editors or the Align… function in the right-click context menu. This makes it easier to manipulate box size appropriately along the pull vector.
The ability to comfortably and safely define simulation box dimensions—aligned with real molecular directions—is one of the small features that prevent large errors.
To learn more or continue with the entire setup, visit the full tutorial at this documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.