When running a center-of-mass (COM) pulling simulation in molecular dynamics, one critical and often overlooked step is setting the simulation box size appropriately. Without enough space in the pulling direction, your simulation can suffer from periodic boundary artifacts, invalidating results even if everything else runs smoothly.
Let’s look into how GROMACS Wizard in SAMSON streamlines this process and helps you define a robust system for controlled COM pulling.
Why box size matters
In COM pulling, you typically pull one group of atoms (e.g., a protein chain) away from another, often in a particular direction like the z-axis. If your simulation box in that direction is too small, the pulled group can appear on the other side of the box due to periodic boundary conditions, leading to a scenario where it interacts with its periodic image. This violates the minimum image convention and makes your simulation unreliable.
Step-by-step Setup in SAMSON
To avoid such issues in SAMSON using the GROMACS Wizard, follow this method demonstrated in the COM Pulling tutorial.
1. Estimate Pulling Distance
Let’s say you’re going to pull chain A from chain B by 5 nm in the z-direction.
2. Compute Necessary Box Size
To meet the minimum image convention, the box length along the pulling axis (z) must be at least twice the pulling length. So for a 5 nm pull, you need at least 10 nm. SAMSON adds an extra buffer (1nm on each side), setting the z-dimension to 12 nm.
3. Use the GROMACS Wizard
- Choose Orthorhombic unit cell.
- Click Compute fitted box.
- Activate Box lengths option and set dimensions:
6.5 nm x 4.5 nm x 12 nm. - Deactivate Center in box and customize the center to
0.5 x 0.5 x 0.2(relative values).
These settings give enough room for the molecule to be pulled without crossing periodic boundaries, while also making visualization and trajectory analysis clearer.
4. Visual Confirmation
Preview the box directly in the Viewport to ensure it surrounds your system appropriately:
Bonus: Aligning the Pulling Direction
Sometimes pulling does not happen neatly along one of the box axes. To simplify your simulation setup, reorient the system in SAMSON using the Align tool:
- Right-click the structure
- Select Move selection > Align…
- Choose appropriate axis or plane
This way, your pulling direction (e.g., between chains A and B) can be aligned with the z-axis of the box, so your force vector doesn’t run at an angle.
Better Simulations, Less Headache
Defining your simulation box might seem minor, but proper setup here can save hours of troubleshooting. By using SAMSON’s interface and safeguards via GROMACS Wizard, you avoid subtle simulation troubles before they happen.
To learn more and follow the complete tutorial, see the original documentation 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.