When preparing coarse-grained (CG) systems for molecular dynamics simulations using the MARTINI force field, one common issue is improper solvation. CG water models like Martini water represent multiple water molecules as one bead (typically 4:1), which drastically changes spatial interactions compared to all-atom models. If left uncorrected, this can produce unrealistic solvent densities or lead to overlapping beads in your periodic box.
Fortunately, SAMSON’s GROMACS Wizard includes a small but important option that solves this pain point: adjusting the van der Waals (vdW) distance for solvent placement during system preparation. This ensures realistic solvation and avoids overlaps that might otherwise derail your simulation from the start.
Why this matters
When adding solvent in GROMACS, the software checks for minimal distances between solute and solvent based on vdW radii. However, for CG models, GROMACS relies on a fixed default value (0.105 nm) since vdW parameters are not defined. That default may be too small for CG systems such as MARTINI, where beads are larger and represent grouped atoms or molecules.
Result: overlapping beads and abnormal local densities.
How to fix this in GROMACS Wizard
GROMACS Wizard makes this easy:
- In the Prepare tab, enable the Add solvent option.
- Click on the gear icon (⚙️) next to it to open solvent options.
- Increase the default vdW distance to 0.21 nm (or test your preferred value).
- Leave other options at their defaults unless you’re targeting specific configurations.
This minor tweak ensures a reliable buffer between solute and solvent. For instance, in the MARTINI model, water beads are roughly 0.47 nm in size — spacing them too closely can invalidate the structure and artificially raise system energy.
Here’s what this looks like in the interface:
Advanced tip: Custom solvents
If you’re using a non-default CG force field or a custom solvent model, SAMSON lets you provide your own solvent definitions. You just need to point the software to the proper coordinate and topology files through the interface.
More details can be found in the official documentation.
Summary
GROMACS Wizard in SAMSON gives you simple but effective control over key solvation settings. For coarse-grained simulations, adjusting vdW distances when adding solvent can eliminate one of the most frustrating early errors in MD system setup.
It’s a small step—but one that improves your chances of a smooth, stable simulation.
To learn more, explore the full tutorial page here: 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.