When preparing a coarse-grained (CG) molecular system for simulation, one often encounters a subtle but important issue: solvent placement. If not handled correctly, solvation can result in overlapping CG beads, leading to instability during energy minimization or early MD phases. This is especially relevant for users working with the Martini force field, where one water bead represents four water molecules.
In GROMACS, van der Waals parameters are essential to place solvent molecules properly. However, for CG models, standard van der Waals distances may not apply. The GROMACS Wizard in SAMSON provides a useful solution to this challenge by giving you full control over solvent placement parameters.
Solvating a CG System in GROMACS Wizard
After loading your CG protein into the GROMACS Wizard and setting up the periodic box, you can choose to Add solvent via the Prepare tab. But here’s the key part: to avoid unphysical overlaps or unstable configurations, you should click the small gear icon 
to configure the solvent settings.
Why Increase van der Waals Distance?
By default, GROMACS uses a van der Waals distance of 0.105 nm. For CG beads, especially for Martini water, this is far too small. Since one Martini water bead represents ~4 water molecules, it’s more realistic—and safer—to use a larger separation during solvation. SAMSON recommends increasing the van der Waals distance to 0.21 nm.
Steps Recap:
- Enable Add solvent in the Prepare tab.
- Click the gear icon to open solvent options.
- Set van der Waals distance to 0.21 nm or higher.
- Leave other parameters as default (unless you are using a custom solvent model).
- Proceed with preparation as usual.
What Happens If You Skip This?
Neglecting this step can result in significant overlaps between solvent and solute beads. These clashes are often not easily visible unless you inspect the structure closely, but they manifest during minimization as failed convergence or high potential energy. It’s better to prevent these problems during preparation by adjusting the solvent placement appropriately.
Using a Custom Solvent?
If you’re working with a custom CG solvent model, ensure that it has proper parameters and take advantage of the Wizard’s configuration options. The documentation includes guidance for using a custom solvent model.
Conclusion
This small step can significantly improve preparation success and reduce trial-and-error debugging during MD simulation setup. GROMACS Wizard makes handling of CG solvents straightforward, especially when using it together with the Martinize2 Extension to generate the system.
To explore more about setting up CG simulations in SAMSON, visit the full tutorial: 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.