When working with coarse-grained (CG) systems in GROMACS using the MARTINI force field, one recurring issue for molecular modelers is solvent bead clashes during solvation. These can lead to non-physical behavior during energy minimization or even cause simulations to crash. If you’ve simulated with the MARTINI model, you’ve likely encountered errors due to overlapping particles or instability during the early steps of your workflow.
The reason? By default, GROMACS assigns a van der Waals (vdW) distance of 0.105 nm between solvent beads. But in MARTINI, a single water bead represents four water molecules, and this default spacing makes CG water beads too close together, creating artificially high density and atomic overlaps.
How to fix this in GROMACS Wizard
The GROMACS Wizard in SAMSON offers a direct way to resolve this by allowing you to customize the solvent options during system preparation.
- Go to the Prepare tab of the GROMACS Wizard.
- Under the solvation section, enable Add Solvent.
- Click the
gear icon next to Add Solvent to open detailed options. - In the popup window, look for the van der Waals distance settings.
- Increase the default vdW distance from 0.105 nm to at least 0.21 nm.
This change ensures proper spacing between MARTINI water beads, reduces artificial overlaps, and helps you avoid common solvating issues before they happen.
Why is this so important?
Not adjusting this van der Waals distance leads to:
- Difficulties during energy minimization
- Non-converging or crashing equilibration runs
- Incorrect density values after solvation
These issues can waste significant time — from troubleshooting failed MD runs to redoing topology steps.
Good to know
This fix applies to any CG system using MARTINI water, not just protein systems generated with the Martinize2 SAMSON Extension. If you’re using a custom force field or solvent model, you can define these settings as well in GROMACS Wizard. This makes the tool flexible for a variety of CG workflows.
To learn more and follow the full tutorial context, see the original documentation: Coarse-grained systems with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.