If you’ve ever run molecular dynamics (MD) simulations with pulling forces—especially center-of-mass (COM) pulling—you’ve likely encountered artifacts caused by poorly defined simulation boxes. These artifacts can significantly compromise the realism of your results. In this post, we’ll explore how you can configure your simulation box in SAMSON’s GROMACS Wizard to avoid boundary issues when pulling molecules apart, specifically using the 2BEG system.
Why Box Dimensions Matter for Pulling Simulations
In MD simulations with periodic boundary conditions, incorrect box sizing can lead to molecules interacting with their own periodic images—a nonphysical outcome. This is particularly problematic in pulling scenarios where significant displacement occurs along a specific axis.
Let’s say we’re pulling chain A 5 nm away from chain B along the z-axis. If your box isn’t long enough in that direction, parts of chain A might reach the edge and interact with its image on the opposite side, violating the minimum image convention.
How to Set the Simulation Box in SAMSON
The GROMACS Wizard in SAMSON offers a user-friendly yet powerful way to define your simulation box parameters. Here’s how to set it up to avoid common pitfalls:
- Select Orthorhombic box type and click Compute fitted box to initialize based on your structure.
- Switch to the Box lengths mode and manually set dimensions. For our 2BEG example, use:
6.5 nm x 4.5 nm x 12 nm. - Uncheck Center in box and set the center to
0.5 x 0.5 x 0.2. This positions the system closer to the bottom along the pulling axis (z-direction) and leaves enough space for movement.
This setup ensures that the 5 nm pulling distance stays well within half the box length (6 nm in this case), meeting the minimum image convention.
You can immediately see the box in the Viewport for verification:
Aligning the Pull Direction
If the pulling direction doesn’t naturally align with a major axis (x, y, z), you can easily reorient the system in SAMSON using the Move selection > Align… feature. This ensures a predictable and clean pulling vector, reducing complexity in interpreting results.
Final Checks Before Proceeding
Before running minimization, equilibration, or production MD:
- Visually confirm box boundaries in the Viewport.
- Ensure your pulling distance is less than half the box length in the pulling direction.
- Optionally, review your parameters in the advanced settings pane for more control.
Taking the time to get your simulation box right during the setup phase can save hours of debugging and, more importantly, ensure your results are physically meaningful.
For a step-by-step guide and more visuals, visit the official COM pulling tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started or explore more features, visit SAMSON Connect.