In molecular dynamics simulations, especially when performing setups such as center-of-mass pulling, one common source of frustration can originate from the simulation box definition. Many users—especially those new to extended systems or periodic boundary conditions—face issues like artificial interactions due to poorly sized boxes or unexpected restraint behavior due to improper positioning of the solute within the box.
This post walks through a core preparatory step from the GROMACS Wizard – COM Pulling tutorial inside SAMSON, explaining how to correctly define the simulation box to ensure robust results when pulling a protein chain in a specific direction.
Why Box Size Matters in Pulling Simulations
When pulling one part of a molecule away from another, the molecule must have enough space to move without interacting with its periodic image. This is essential to avoid artifacts due to the minimum image convention, which states that in periodic simulations, atoms only interact with the closest image of other atoms.
If the system is pulled more than half the box size along the pulling direction, it may start interacting with its own periodic replica—compromising the physical relevance of the results.
Example: Pulling Chain A from Chain B
In this tutorial example, the user aims to pull chain A away from chain B in the z-direction by 5 nm. To avoid self-interaction during the pulling, the length of the box along the z-axis is set to at least twice this distance, with additional margins:
- Pull distance: 5 nm
- Minimum box size along z: 10 nm
- Final box z-length: 12 nm
The box dimensions used are 6.5 nm x 4.5 nm x 12 nm, with the system centered asymmetrically using a relative center-of-mass position at 0.5 x 0.5 x 0.2. This ensures the pulled chain has room to move upward in z without quickly approaching the clone below it.
Step-by-Step Instructions
- Choose the Orthorhombic unit cell and click “Compute fitted box” to estimate the initial box size using system geometry.
- Manually override the dimensions with
6.5,4.5, and12.0nm box lengths for the x, y, and z directions, respectively. - Deactivate the “Center in box” option.
- Specify a center at
0.5,0.5,0.2on the relative scale (0 to 1).
Through the graphical interface in SAMSON, this setup is made visible in real-time:
This spatial awareness helps avoid launching a long simulation only to later discover overlapping images and invalid energy profiles.
Takeaway
Correct box definition is about balancing system size, computational resources, and the physics of periodic boundary conditions. Especially in sensitive simulations like COM pulling, taking the time to align the pulling direction with box axes and setting correct margins can save significant downstream troubleshooting effort.
To learn more about this and continue with energy minimization, equilibration, and COM pulling simulation, visit the full tutorial: 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.