Preparing a coarse-grained system for molecular dynamics (MD) simulations can be surprisingly tricky — especially when it comes to solvation. When you’re using MARTINI v.3.0.0 force field models in SAMSON’s GROMACS Wizard, one of the most frustrating issues you might encounter is related to improper solvation density due to van der Waals distance defaults in GROMACS.
Here’s what usually happens: you’re working with a CG model, everything seems fine, but once you add solvent molecules and launch a simulation, you notice that the solvent density is way off. The culprit? GROMACS doesn’t define van der Waals distances for CG beads, and ends up using a default value (0.105 nm), which can allow solvent molecules to clash or overlap inappropriately. That’s especially problematic with MARTINI’s water beads, since each bead represents four water molecules 🧊🧊🧊🧊.
Solvating CG Systems Correctly
When you’re adding solvent to your system in the Prepare tab of GROMACS Wizard, there’s a simple but important step you need to follow:
- Check the Add solvent box to enable solvation options.
- Click the gear icon (
) next to the box to access advanced solvent options. - In the pop-up dialog, locate the van der Waals (vdW) distance parameter and increase it manually from the default
0.105 nmto at least 0.21 nm. This helps GROMACS place water beads at a safe distance from other beads.
By updating this value, you reduce bead overlap and ensure physical plausibility in the solvation structure. This is especially crucial for proper behavior during equilibration and production MD runs.
While it might seem like a small tweak, failing to adapt the vdW distance can have cascade effects through the entire simulation workflow. In worst cases, you may see instabilities, high energies, or even simulation crashes.
What About Custom Solvents?
If you’re not using the default Martini water, SAMSON also supports custom CG solvents. The Wizard provides options for supplying your own solvent model if needed. Just follow this guide if you need custom solvent behavior tailored to your specific use case.
One Last Tip
Don’t forget: if you’re planning to neutralize your system or add salt, this also depends on the presence of a solvent. Ions are usually added by replacing solvent beads, so solvation is a prerequisite for any ionic adjustments. Read more about that in the documentation’s section on neutralizing the system.
Solving this specific solvation issue means your MARTINI CG simulations can proceed with fewer surprises and more stability, reducing wasted time and troubleshooting.
Learn more about preparing MARTINI CG systems in GROMACS Wizard in the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.