When setting up a molecular dynamics (MD) simulation involving pulling, a frequent source of frustration among researchers is improper definition of the simulation box. The consequences? Artifacts due to periodic boundary conditions — from nonphysical interactions to misleading energy profiles. Here’s how to correctly set up the simulation box in SAMSON’s GROMACS Wizard for center-of-mass (COM) pulling, helping you avoid common pitfalls and get the results your system actually deserves.
📦 Why the Box Size Matters
In COM pulling simulations, you apply a force to pull one group of atoms (e.g., a protein chain) away from another. If your box isn’t long enough in the direction of pulling, the molecule might interact with its periodic image during the simulation. This violates the assumption of isolated pulling and can dramatically distort results.
This is where the minimum image convention comes into play — any particle should only interact with the nearest image of another particle, which essentially requires your pulling coordinate to remain within half the box length along that direction.
How to Set It Up in GROMACS Wizard
1. Choose the Box Shape
Pick the Orthorhombic unit cell. In SAMSON’s GROMACS Wizard, this can be done in the Prepare step. Click Compute fitted box to generate a starting box size based on the molecular system.
2. Adjust the Box Dimensions
Let’s say you plan to pull chain A away from chain B along the z-axis by 5 nm. You’ll want the z-length of the box to exceed twice that distance (to allow for pulling and avoid interactions with the periodic image). A safe choice here is:
6.5 nm x 4.5 nm x 12 nm
This gives your system breathing room along the z-axis, meeting the convention while leaving extra space to avoid edge effects.
3. Position the System
Next, adjust where your system sits inside the box. Deactivate the Center in box option and place the system at 0.5 x 0.5 x 0.2, meaning you’re shifting the structure lower along the z-axis. This gives your pulled chain room to move upwards during the simulation, without running into itself across the periodic boundary.
Tip: If your pulling direction is not aligned with the main axes, you can reorient the system using move editors or by right-clicking and choosing Move selection > Align... in SAMSON.
4. Preview and Validate
Once these parameters are set, you can visualize the box-size and position directly in the Viewport. You should see plenty of free space in the pulling direction (z-axis in this case).
🔍 Common Mistakes to Avoid
- Incorrect alignment: Pulling off-axis can lead to ambiguous results unless the system is oriented properly.
- Box too small: Anything less than twice the pulling distance (plus safety buffer) invites interactions with periodic images.
- Centering the system: Automatically centering it often leaves equal space in all directions — not ideal for directed pulling.
🧪 Summary
Pulling simulations can deliver valuable insight into molecular mechanics, but they require meticulous box configuration. SAMSON’s GROMACS Wizard makes it easier to visualize and manipulate these parameters — provided you know what to look for.
For a step-by-step guide through the full procedure, including minimization and COM pulling configuration, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.