Working with coarse-grained (CG) models is a common strategy for simulating larger molecular systems with reduced computational cost. However, when preparing these systems for molecular dynamics (MD) simulations, one subtle but critical issue often trips up even experienced modelers: the solvent configuration.
In particular, GROMACS does not define van der Waals (vdW) distances for CG beads by default. This oversight can result in overlapping solvent molecules or poorly packed solvent environments—leading to unstable simulations. The good news: the GROMACS Wizard Extension in SAMSON offers a streamlined way to resolve this.
This post guides you through the process of solvating CG systems properly, using the recommended settings in the GROMACS Wizard. These steps will help ensure a stable and realistic solvation environment so you can move forward confidently with minimization, equilibration, and production MD.
Why vdW Distance Matters
Martini-based CG water models represent multiple water molecules as a single bead—typically four. These beads are physically larger than atoms in all-atom models, meaning the default 0.105 nm vdW distance used by GROMACS is usually too small. This can lead to solvent molecules being placed too close to solute atoms or each other, creating unfavorable starting configurations.
Solvation Settings in SAMSON’s GROMACS Wizard
In the GROMACS Wizard, when you select the option to Add solvent, you can access solvation details by clicking the small gear icon next to the checkbox:
This opens a panel where you can adjust key parameters, including the crucial van der Waals distance. By default, this is set to 0.105 nm, but for Martini CG systems, it’s recommended to increase it to 0.21 nm to minimize steric clashes and improve solvent packing.
Here’s a quick checklist:
- Enable Add solvent.
- Click the gear icon to access the solvation preferences.
- Set vdW distance to ~0.21 nm.
- Leave other settings at their defaults unless your system requires custom values.
Why 0.21 nm? While there isn’t a universally optimal number, this value generally avoids overlaps while maintaining appropriate solvent density for Martini-level CG models.
Custom Solvent Models
If you’re working with a non-default CG solvent model, SAMSON allows you to provide your own solvent files. This may be relevant for specific applications, such as membrane systems or mixed solvents. See the section Using a custom solvent model for more.
Putting It All Together
After setting up your system folder and confirming the Martini v.3.0.0 force field is selected, these solvation settings are the final touch before you move to the next steps: ion addition, box optimization, or simulation runs.
Taking a moment to configure the solvent vdW distance can save hours—in simulation time and troubleshooting frustration.
To learn more—including how to add ions, modify periodic box parameters, and prepare input for MD steps—visit the full documentation page here:
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.