When preparing a molecular dynamics simulation involving pulling—such as center-of-mass (COM) pulling—one of the most overlooked yet critical steps is correctly defining the simulation box size. A common pitfall for modelers is encountering artifacts due to improper box dimensions, especially when working with periodic boundary conditions.
In the GROMACS Wizard in SAMSON, the process of defining the simulation box is not only visual but also flexible, helping you anticipate and avoid common mistakes.
Why Box Size Matters
When using periodic boundary conditions, if the box is too small in the pulling direction, the molecule being pulled might interact with its own periodic image. This can produce artificial forces and skew the dynamics, leading to misleading or invalid results.
According to the minimum image convention, the maximum distance between two interacting particles must be less than half the box size in any direction. This implies that the total pulling distance should be less than half the box length along the pulling axis—even more space is recommended for safety.
How to Set Up the Box in SAMSON
If you’re following the COM pulling protocol in SAMSON’s GROMACS Wizard, and plan to pull chain A 5 nm away from chain B along the z-axis, you need to ensure your box size allows for this motion without violating periodic constraints.
Here’s how it’s done:
- Select the Orthorhombic unit cell.
- Click Compute fitted box to obtain initial dimensions based on the system size.
- Set box lengths manually to:
6.5 nm x 4.5 nm x 12 nm
This gives 2 nm clearance beyond the 10 nm (double the pull distance) recommendation. - Deactivate Center in box and set the center to:
0.5 x 0.5 x 0.2
This ensures the molecule is positioned lower in the box, providing more space in the pulling direction.
The visual feedback in the Viewport helps confirm that your molecular system is well-positioned inside the simulation box and prevents you from having to guess spatial arrangements.
Visual Guide
The screenshot below illustrates the adjusted box with proper dimensions and centered positioning for pulling simulations:
Tips
- If pulling geometry is not aligned with XY or Z axes, reorient your system using context menu options (Right-click → Move selection → Align…).
- Always compute an initial box and adjust manually rather than relying on defaults when pulling is involved.
Getting the box size right can save hours of rework and avoid erroneous results. It’s not just about space—it’s about accuracy, avoiding unwanted interactions, and preserving the physical meaning of your simulation.
For a complete step-by-step tutorial on setting up a COM pulling simulation in SAMSON using the GROMACS Wizard, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.