When setting up a coarse-grained (CG) molecular simulation, one of the most frequent stumbling blocks for modelers is improperly defined boundary conditions. A misconfigured periodic box can lead to unphysical interactions and ultimately unreliable results. In CG systems — particularly those based on the MARTINI force field — the box setup becomes even more crucial due to the larger effective size of beads and the absence of atomic-level van der Waals data.
Let’s take a closer look at how you can configure your periodic box in SAMSON’s GROMACS Wizard when preparing a CG system, such as a soluble protein generated with Martinize2.
Loading Your System and Building a Periodic Box
Once you’ve generated your CG model, simply switch to the Prepare tab in GROMACS Wizard. Point to your system folder containing the CG .pdb and .top files.
After selecting the appropriate folder, the Wizard will detect and display your structure and topology files. Importantly, when you click Load on your PDB file, GROMACS Wizard will automatically compute a periodic box.
At this point, the Wizard also detects if the model uses the MARTINI v.3.0.0 force field and configures it accordingly, helping you avoid mismatches.
Customizing Box Shape and Size
Don’t stop at the default box. To ensure your simulation’s accuracy and efficiency, you may want to tweak its characteristics. If your solute is relatively spherical, switching the unit cell type to a Rhombic dodecahedron can save computational resources by reducing the number of solvent beads added.
Also, consider adjusting the solute-box distance. A generally accepted minimum is 1 nm, which helps prevent unwanted interactions between periodic images. CG beads, due to their abstracted representation, benefit from this added spacing.
Solvent and Ion Considerations
If you’re adding solvent, make sure to increase the default van der Waals distance to values like 0.21 nm. Since GROMACS lacks van der Waals data for CG systems, using the default of 0.105 nm may lead to overlapping beads and incorrect solvation densities.
Ion addition (for charge neutralization or salt concentration control) is another key step affected by box dimensions. Ions are added by replacing solvent molecules, so solvent setup must come first.
Putting It All Together
After adjusting the periodic box, solvent parameters, and ion setup, just hit Prepare. You’ll get a fully constructed system ready for minimization, equilibration, and production MD.
Learning to fine-tune your periodic box setup using GROMACS Wizard can save you time and help you avoid common issues downstream. It’s not just about putting your system in a box — it’s about putting it in the right box.
To dive deeper, check out the full tutorial section on coarse-grained systems: https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.