When setting up a molecular dynamics simulation involving pulling—especially center-of-mass (COM) pulling—most modelers know that choosing a suitable periodic box is essential. However, it’s also one of the most frequent sources of avoidable simulation artifacts due to improper box size or misalignment with the pulling direction.
Let’s focus on a practical example: setting up the periodic box for pulling chain A from chain B in a protein complex using the GROMACS Wizard in SAMSON. This step may seem minor, but it is crucial for ensuring physically valid simulations and avoiding errors arising from periodic boundary conditions.
The pulling in this tutorial happens along the z-axis for a distance of 5 nm. According to the minimum image convention, the box length in the pulling direction needs to be at least twice that distance, i.e., 10 nm. However, additional space is recommended to avoid boundary interactions. In this setup, the z-dimension of the box is padded to 12 nm, as shown below:
A key option here is choosing an orthorhombic unit cell and computing a fitted box based on the system’s dimensions. Then, we adjust the box manually to the target size: 6.5 nm × 4.5 nm × 12 nm.
Most users activate the Center in box checkbox by default. For pulling simulations, this can be a problem if the structure ends up too centered and the pulled group reaches the box boundary prematurely. Instead, deactivate this option and shift the center of the system toward one end of the box in the pulling direction. In this example, the center is set to 0.5 × 0.5 × 0.2 of the box size, offering 10 nm of room in the z-direction to accommodate the pulling distance.
Visually confirming the box size and position in the SAMSON Viewport is recommended. This helps ensure there is enough space to apply pulling forces without wrapping molecules back on themselves via periodic images, which can cause nonphysical artifacts.
If your pulling vector is not aligned to x, y, or z, you can easily realign the system in SAMSON by right-clicking on the molecular structure and using Move selection > Align… or through move editors—these options allow you to set the pulling direction precisely as needed.
Skipping or misconfiguring this step could mean wasted hours (or worse) when simulations crash, or results become invalid. Spending a few extra minutes to correctly define your box and adjust the orientation saves time and improves the quality of your simulation data.
To learn more about this workflow and the complete tutorial on COM Pulling with GROMACS Wizard in SAMSON, 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.