Setting Up Your COM Pulling Simulation: Box Size and Orientation Explained

When setting up molecular simulations involving pulling, especially center-of-mass (COM) pulling in GROMACS, an often overlooked step can significantly affect the accuracy and reliability of your results: correctly defining the periodic simulation box. In this blog post, we’ll walk through how to configure the simulation box in SAMSON using the GROMACS Wizard Extension to account for pulling in the z-direction, and why it matters.

Why box definition matters in COM pulling

In COM pulling simulations, we apply forces along a defined direction to separate molecular groups. When done in a periodic boundary condition (PBC) environment, forces can interact across box images unless the setup strictly respects the minimum image convention. This means your pulling distance should always be significantly smaller than half the dimension of the box in the pulling direction. Otherwise, you’ll risk “pulling into a neighbor box,” which distorts results and interpretation.

Orient your system first

Before defining your box, make sure the pulling direction aligns with one of the main axes (x, y, or z). SAMSON provides intuitive tools to reorient your molecule:

  • Use Move Selection > Align… (accessible via right-click) to align chains to the z-axis.
  • Or manually rotate the structure in the Viewport to align with your intended pulling axis.

This step simplifies interpreting results and setting appropriate box dimensions.

Set up your simulation box appropriately

For this example, suppose we want to pull chain A 5 nm away from chain B in the z-direction. We must ensure the box is large enough to accommodate this displacement without interactions through periodic boundaries.

Here’s how we define the box in SAMSON:

  1. Select Orthorhombic unit cell shape.
  2. Click Compute fitted box to estimate base dimensions.
  3. Enable Box lengths and manually set the dimensions to:
    6.5 nm x 4.5 nm x 12 nm
    This ensures the z-dimension (12 nm) is more than twice the 5 nm pulling distance.
  4. Uncheck Center in box and position the molecule with COM at 0.5 x 0.5 x 0.2 of box size. This offsets the system toward the bottom of the z-axis, leaving room for upward pulling.

Periodic box parameters

You’ll immediately see the box rendered in SAMSON’s Viewport, helping you ensure the setup matches expectations.

COM Pulling box in the Viewport

Troubleshooting Tips

  • If your trajectory shows overlap or abrupt changes in force, revisit the box size.
  • Double-check system orientation before setting the box length.
  • Use visual inspection of the Viewport to verify physical plausibility of pulling space.

Conclusion

Although it’s easy to skip over, properly configuring the simulation box is critical for successful COM pulling simulations. Getting this right ensures compliance with the minimum image convention, avoids artifacts in force profiles, and ultimately yields more meaningful insights.

To see a complete walkthrough and try it yourself, visit the full tutorial:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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