Preparing coarse-grained (CG) systems for molecular dynamics (MD) simulations can often feel like stepping through a minefield of small issues that lead to problematic simulations. One pain point that many molecular modelers encounter is setting up solvation properly when working with CG models, such as those created using the MARTINI 3.0.0 force field. Why? Because these models operate on a level of abstraction where each bead represents multiple atoms, and this directly impacts how solvation should be handled.
If you’ve ever seen overlapping beads, unwanted voids, or unexpected dynamics during your CG simulations, there’s a good chance that the issue started with an inadequate default setup in your preparation pipeline.
Why van der Waals Distance Matters for CG Solvation
Most solvers—like GROMACS—use van der Waals (vdW) distances to determine how close solvent molecules can be to the solute. Atomistic models usually have well-defined vdW parameters for all atoms. However, GROMACS does not define them for CG beads by default. That means during solvation, GROMACS falls back to a default vdW distance of 0.105 nm—which works fine for atom-level water, but not for CG water beads like those in MARTINI (each representing four actual water molecules).
The result: water beads are placed too close to other beads, leading to steric clashes, low-quality dynamics, or worse—unstable simulations.
Solving It with SAMSON’s GROMACS Wizard
In the GROMACS Wizard integrated within the SAMSON platform, there’s an elegant solution to this issue.
When you reach the point of adding solvent to your system, click on the gear icon next to Add solvent to access the solvation settings:
Then, in the pop-up window, increase the van der Waals distance to around 0.21 nm. This value gives a more appropriate spacing for the MARTINI water beads:
Why 0.21 nm? It approximates the physical size of the bead and avoids overlaps, giving your CG water model the space it needs while maintaining the correct density.
Tips for Consistent Setup
- ▶️ Always verify that the force field is correctly set to
martini_v.3.0.0. SAMSON’s GROMACS Wizard does this automatically if you used Martinize2 to generate your CG system. - 🧭 Make sure you changed the periodic box to a space-filling unit cell (like a rhombic dodecahedron) and adjusted solute-box distance to at least 1.0 nm.
- ⚠️ Remember that ions are added by replacing solvent molecules. So you need to add solvent first before attempting to neutralize or set salt concentration.
Visual Checkpoint
After making these changes, your solvation step should result in a clean, overlap-free system. Here’s a snapshot of a properly prepared CG system:
Conclusion
Solvation in CG systems may feel trivial—just another checkbox in the setup. But controlling the vdW distance is a small tweak with significant impact. It simplifies post-processing, improves realism, and reduces the risk of simulation failure. Combined with automatic detection and sensible defaults in SAMSON’s GROMACS Wizard, this step can become routine rather than a recurring problem.
Learn more from the original documentation and explore the full workflow.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.