When preparing a molecular dynamics simulation involving center-of-mass (COM) pulling, one challenge that often arises is correctly sizing the simulation box. Too small, and you risk violating periodic boundary conditions; too large, and computational resources are unnecessarily wasted. This blog post explains a straightforward method to define the pulling box in SAMSON’s GROMACS Wizard for simulations involving chain separation – using a specific example: pulling chain A from chain B in the 2BEG system.
Why Does Box Size Matter?
In COM pulling, you apply a force to one group while restraining another. If you don’t give the system enough room along the pulling direction, the pulled group might interact with its own periodic image. This not only invalidates results but may also cause the simulation to crash or behave unpredictably due to artifacts from the minimum image convention.
Box Setup in SAMSON
In the GROMACS Wizard, setting an appropriate box is part of the Preparation step. Let’s consider pulling chain A from chain B by 5 nm along the z-axis.
The rule of thumb: the distance between periodic images should be at least twice the pulling distance. In this case, 5 nm x 2 = 10 nm. To be safe, SAMSON adds 1 nm padding on both ends, making it 12 nm in the pulling direction (z).
- Box dimensions used:
6.5 nm x 4.5 nm x 12 nm - Pulling direction: z
- Box type: Orthorhombic
- Center of mass position inside the box:
0.5 x 0.5 x 0.2
The 0.2 value for the z-component of the center positions the system close to one end of the box, allowing sufficient space along the positive z-axis for the pulling to occur. You can see a visualization of the box directly in SAMSON’s viewport:
Tips for Alignment
If your desired pulling direction isn’t already aligned with one of the Cartesian axes, you can use SAMSON’s alignment tools. Right-click your structure and select Move selection > Align… to orient it with respect to an axis or a plane. This is especially helpful when your molecule is orientated arbitrarily.
Tip
Remember, the box should always respect the minimum image convention. This means that the pull distance along an axis must be LESS than half the box’s length in that direction.
Conclusion
Ensuring enough room for your COM pulling simulations isn’t about guesswork—SAMSON’s GROMACS Wizard makes it easy to define and visualize the correct box dimensions based on your setup. Always take into account your pulling direction and distance, apply the appropriate box size, and you’re one step closer to a reliable simulation.
To learn more about COM pulling in SAMSON’s GROMACS Wizard, visit the full documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.