One of the most common sources of simulation issues in molecular dynamics is the improper definition of the simulation box during setups involving pulling between molecular chains. This often results in unintended interactions across periodic boundaries, leading to inaccurate results or simulation failures.
If you’re using the GROMACS Wizard in SAMSON for a center-of-mass (COM) pulling simulation like pulling chain A away from chain B in a protein dimer, your simulation setup must obey GROMACS’s minimum image convention. This requires that the pulling distance stays under half the box size along that direction—including periodicity.
Here’s a simple setup tip that can prevent many downstream problems: always leave enough room in the pulling direction. In the COM pulling example from the GROMACS Wizard tutorial, we’re pulling chain A 5 nm from chain B along the z-axis. This means the box length in z must be at least twice that distance (10 nm) to avoid overlap due to periodic boundaries. Preferably, add a buffer on both sides. In this tutorial, the box is set to 12 nm in the z-direction: safe and simulation-ready 👌.
Follow these steps to adjust your box size in the GROMACS Wizard:
- Select the Orthorhombic box type.
- Click Compute fitted box to get an initial volume estimate.
- Use the Box lengths fields to manually enter the desired size. For this example:
6.5 nm x 4.5 nm x 12 nm. - Deactivate Center in box and instead manually define the center with normalized coordinates. Set as:
0.5 x 0.5 x 0.2(0 to 1 scale), so that the system starts near the bottom of the z-dimension, allowing it space to be pulled upward.
This logic holds for any dimensional pulling or umbrella sampling projects: plan ahead by considering the physical motion range and leave generous room within the box, especially in the pulling direction.
The GROMACS Wizard also offers visualization support: you can see the box and the molecular system directly in the Viewport.
💡 Tip: If your pull direction isn’t aligned with the standard x/y/z axes, you can reorient the system using SAMSON’s move tools or by aligning selections via context menu options.
Proper box sizing ensures your COM pulling simulation runs smoothly and gives interpretable results without artificial periodic effects. You can learn more and follow the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net