When setting up coarse-grained (CG) systems for molecular dynamics simulations with GROMACS, one common source of instability and frustration is poor solvation—especially when solvent molecules are placed too close to solute atoms, causing steric clashes. Fortunately, SAMSON’s GROMACS Wizard offers a straightforward solution to this issue by allowing you to adjust the default van der Waals distance used during solvation. This simple tweak can save hours of debugging and improve simulation stability right from the start.
Why it matters: CG systems need space
In atomistic models, van der Waals radii are defined for most atoms, guiding solvation algorithms to avoid overlaps. However, in coarse-grained systems (like those based on the MARTINI force field), such definitions are generally missing because CG beads represent groups of atoms—often 4 water molecules per bead. When GROMACS processes these beads without this information, it defaults to a van der Waals distance of 0.105 nm, which is often too small for CG beads. The result? Overcrowded solvent shells, unnatural densities, and simulation crashes during the equilibration or minimization steps.
Solving the issue in GROMACS Wizard
GROMACS Wizard in SAMSON offers a clean UI-based workaround:
- In the Prepare step of GROMACS Wizard, check the Add solvent option.
- Click the small gear icon next to the checkbox to open solvent options.
- Change the van der Waals distance from the default
0.105 nmto a higher value—0.21 nmis a recommended starting point. - Leave other options at their default settings unless you have specific needs.
This adjustment ensures that solvent beads are inserted with enough spacing to prevent overlaps, better representing packing density and avoiding solute-solvent clashes.
When and where this is useful
This fix is particularly useful if:
- You use the Martinize2 Extension to generate CG systems with the MARTINI 3.0 force field.
- You encounter crashes during neighbor searching or energy minimization steps related to steric clashes.
- You observe unnatural solvent densities around your solute.
It’s a minor change but has a major impact on the stability of your systems. This example shows how user-friendly design elements in GROMACS Wizard can improve simulation workflows by providing context-aware parameters.
Going further
Want to use a completely custom CG solvent model? GROMACS Wizard also supports that. Take a look at the custom solvent model section in the full documentation.
For a full walkthrough on preparing coarse-grained systems using GROMACS Wizard in SAMSON, see the full tutorial 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 get SAMSON at https://www.samson-connect.net.