One common frustration for molecular modelers preparing coarse-grained (CG) systems for molecular dynamics simulations is dealing with solvated structures where solvent beads overlap with solute atoms. These clashes often cause failed simulations or unphysical behavior. The root cause? The default van der Waals (vdW) distance used during solvation is too small for CG models.
Solving this issue in SAMSON using the GROMACS Wizard is straightforward—but only if you know where to look. This blog post guides you through fixing this pain point by properly configuring solvent parameters in CG systems, ensuring more stable and realistic starting structures for your simulations.
Why Does This Happen?
Coarse-grained models like those based on the MARTINI force field treat groups of atoms as single interaction sites or “beads.” In MARTINI water, one bead typically represents four water molecules. The default vdW distance used by GROMACS when placing solvent molecules is approximately 0.105 nm, which works well for atomistic models—but it’s far too small for CG beads. As a result, solvent can be placed too close to solute atoms, causing steric clashes and artifacts in the simulation.
Below is what the solvent options panel looks like in the GROMACS Wizard inside SAMSON:
How to Fix It
When using the GROMACS Wizard to solvate a CG system, simply follow these steps:
- Check the “Add solvent” option in the Prepare tab.
- Click on the gear icon next to it to access advanced solvent options.
- Increase the van der Waals distance to a more suitable value like 0.21 nm.
This adjustment ensures better packing of solvent beads and reduces the likelihood of atom overlaps or unphysical interactions. The choice of 0.21 nm is a recommended guideline, as it offers a reasonable distance to prevent overlaps while ensuring a realistic solvent density for CG models.
Here is the dialog you’ll be working with:
Advanced Tip: Use a Custom Solvent Model
If you’re working with a unique coarse-grained force field or want even more control over solvent properties, SAMSON also allows you to provide a custom CG solvent model. You can learn more about doing that in the GROMACS Wizard – Using a custom solvent model documentation page.
Why It Matters
By simply adjusting the vdW distance, you prevent early-stage simulation instabilities, save time debugging failed runs, and get a better starting point for energy minimization and equilibration. It’s a small tweak that can make a significant difference, especially if you’re performing systematic studies or high-throughput screening simulations.
Learn More
To dive deeper into coarse-grained system setup with GROMACS Wizard in SAMSON, visit the full tutorial at this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.