When preparing molecular dynamics simulations that involve center-of-mass (COM) pulling — such as separating chains in a protein complex — one of the most common sources of error is the incorrect definition of the simulation box. The consequences? Unexpected interactions due to periodic boundary conditions, inaccurate distance constraints, or simulations that fail outright. This blog post will walk you through the best practices for defining an appropriate simulation box using the GROMACS Wizard in SAMSON.
Why Box Size Matters in Pulling Simulations
In periodic systems, atoms that move too close to the edge of the simulation box may start interacting with their periodic images — a phenomenon known as artifact interaction. Pulling one part of a molecule away from another, as in the case of chain A from chain B, requires careful planning of the box dimensions to avoid such issues.
The rule of thumb: the box dimension along the pulling direction should be more than twice the pulling distance, due to the minimum image convention.
Step-by-Step: Defining the Box
For the 2BEG system used in this tutorial, we want to pull chain A 5 nm away from chain B in the z-direction. Here’s how we set the box:
- Select an Orthorhombic unit cell.
- Click Compute fitted box to get a baseline size matching the molecular structure.
- Adjust the dimensions by choosing Box lengths and setting them to
6.5 nm x 4.5 nm x 12 nm. - Uncheck Center in box and instead manually set the center to
0.5 x 0.5 x 0.2— biasing the starting position downward on the z-axis to maximize forward pulling space.
This setup provides enough buffer (2 nm) in the direction of pulling to satisfy the minimum image convention while giving flexibility for molecular movement.
What If You Need a Different Pull Direction?
If the pulling direction isn’t aligned with the main Cartesian axes, no problem. SAMSON allows you to reorient the molecular system. Just right-click the structure and choose Move selection > Align…. You can also use SAMSON’s move editors for more control.
Wrapping Up
A well-defined box is the silent enabler of a robust pulling simulation. It’s easy to overlook, but taking the time to configure it right can save you hours of troubleshooting later. Whether you’re new to GROMACS or switching to SAMSON for more visual control, following these practices ensures your simulations run smoothly and your results are physically meaningful.
To explore the full COM pulling tutorial in SAMSON, visit the original documentation: 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.