When performing molecular dynamics simulations involving center-of-mass (COM) pulling, failing to correctly define the simulation box can lead to artifacts—especially when periodic boundary conditions come into play. One common challenge molecular modelers face is ensuring that enough space exists in the pulling direction. This blog post walks you through how to define a simulation box for COM pulling with GROMACS Wizard in SAMSON while respecting the minimum image convention.
Why the Simulation Box Matters in Pulling Simulations
If you’re pulling one part of a molecular system (say, a protein chain) away from another, you’re generating significant displacement in a particular direction. In periodic systems, that pulled part could interact with itself due to the way simulation boxes repeat. This is where the minimum image convention becomes essential: to avoid artifacts, the pull distance must be less than half the box length in the pulling direction.
For example, if you’re planning to pull Chain A away from Chain B by 5 nm, you need a box with at least 10 nm of length in your pulling axis—plus some buffer just to be safe.
How to Set the Simulation Box in SAMSON
Here’s how the GROMACS Wizard in SAMSON helps you configure the box properly for a pulling simulation:
- Choose Orthorhombic unit cell.
- Click Compute fitted box to let SAMSON provide a good initial estimate for the box.
- Switch to Box lengths and manually update them as follows:
- x: 6.5 nm
- y: 4.5 nm
- z: 12 nm (to accommodate a 5 nm pulling distance)
- Deactivate Center in box and manually set the system’s center to
0.5 x 0.5 x 0.2of the box dimensions. This moves the molecules closer to one edge, maximizing usable space in pulling direction.
If your pulling direction isn’t nicely aligned with x, y, or z, SAMSON helps there too. You can use the move editors or right-click on your structure and select Move selection > Align… to orient the system along a principal axis. This makes spacing and directionality much easier to manage.
Visual Feedback in the Viewport
SAMSON offers a helpful visualization of the simulation box directly in the Viewport. This allows you to visually confirm that the system appears correctly centered and appropriately spaced—as shown below:
A Key Tip You Might Miss
Adding 1 nm of buffer space on each side (making a total of 12 nm for a 5 nm pull) may seem excessive, but it helps conform to the minimum image convention and avoids boundary issues even if your chain gets overly mobile. Think of it as molecular elbow room.
Conclusion
A poorly sized simulation box is one of those subtle mistakes that can cost you hours of wasted simulations. With GROMACS Wizard in SAMSON, setting up a safe, appropriately-sized box is straightforward, visual, and integrated—ensuring your pulling simulations go as planned.
To learn more about the full COM pulling tutorial, check out the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.