When setting up a coarse-grained (CG) simulation with the MARTINI force field in GROMACS, many modelers run into a subtle but frustrating issue: unrealistic solvent packing that leads to simulation artifacts, often caused by solvent molecules overlapping with the solute or each other. This is due to inappropriate van der Waals distances used when solvating CG systems.
If you’ve ever found your simulations behaving strangely right after solvation — excessive pressure, fast destabilization, or weird water behavior — this could very well be the reason. GROMACS, by default, uses a van der Waals distance of 0.105 nm (appropriate for atomistic systems), which is much too small when using MARTINI models where each bead has a larger effective size. Fortunately, SAMSON’s GROMACS Wizard offers a simple solution.
Solvating CG Systems the Right Way
Using the GROMACS Wizard in SAMSON, here’s how you can correctly solvate your MARTINI CG system and avoid the typical pitfalls:
- Once your CG system is loaded in the Prepare tab, enable the Add solvent checkbox.
- Click on the gear icon (
) next to it to access solvation options. - In the options window, manually increase the default van der Waals distance to better match CG resolution. For MARTINI, a good value is
0.21 nm, which avoids spatial overlaps while maintaining realistic solvent density.
This small adjustment is crucial: MARTINI water beads represent four water molecules, and their effective size is significantly larger than individual atoms. The increased distance allows them to be properly spaced and leads to more stable simulations.
Why GROMACS Defaults Don’t Work
GROMACS is primarily atomistic by design and defaults to using atomic-scale parameters. When it can’t find bead-specific values (as is the case for many CG force fields), it falls back to generic values intended for atomic models. This is perfect for all-atom simulations but can be problematic for CG setups like MARTINI.
What this means in practice is that if you’re not adjusting the van der Waals distance during solvation:
- Your beads may be placed too close together
- This leads to overlaps, high local pressure, and instability
- Artifacts might not show immediately but can impact equilibration and production runs
So if you experience simulation crashes right after solvation or end up with inaccurate solvent densities, check your solvation settings — this simple change might save hours of troubleshooting.
Advanced Tip: Custom Solvent Models
If you need to use a solvent model other than the default MARTINI water, SAMSON’s GROMACS Wizard also allows you to plug in your own CG solvent model and define parameters suitable for it. This is helpful for special-purpose solvents in membrane simulations or other non-standard environments.
More information on this can be found in the Custom Solvent Model section.
Conclusion
Solvating coarse-grained systems isn’t difficult, but it does require attention. Adjusting the van der Waals distance when adding solvent is one of those small yet critical steps that often gets overlooked. Fortunately, SAMSON’s GROMACS Wizard makes this much easier by providing intuitive controls through a graphical interface.
Learn more in the full Coarse-Grained Systems tutorial
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.