When setting up coarse-grained (CG) molecular dynamics (MD) simulations in GROMACS using the MARTINI force field, one of the most common frustrations is solvent clashes. These issues often arise not from user error, but from a default behavior: GROMACS applies van der Waals parameters that do not match the scale and nature of CG systems where each bead may represent multiple atoms or even molecules. This can lead to overlaps between solute and solvent, affecting density and stability once the simulation begins.
If you’re using the GROMACS Wizard Extension inside SAMSON, there’s a simple yet often overlooked fix for this.
Why the Default van der Waals Distance Falls Short
When solvating a CG system, GROMACS uses a default van der Waals distance of 0.105 nm. In CG models like those based on MARTINI, water beads represent 4 real water molecules. That makes this default spacing too small, leading to potential overlaps between water beads and solute, or between beads themselves.
The Solution: Adjust the Default Spacing
Use the GROMACS Wizard’s solvation options to increase the van der Waals spacing. A safe choice is typically around 0.21 nm. Here’s how to do it:
- In the Prepare tab of the GROMACS Wizard, check the Add solvent option.
- Click the gear icon
next to it. - In the pop-up Solvent Options dialog, increase the van der Waals distance to 0.21 nm.
That’s it. This small modification ensures that GROMACS won’t place water beads too close to other beads, preventing unrealistically high local densities and simulation instability.
When Should You Apply This?
Always. Unless you’ve defined custom van der Waals parameters for CG solute-solvent interactions (which many users don’t), this tweak is universally helpful for MARTINI and similar CG force fields.
Extra Tip: Solvent Model Flexibility
If you’re using a custom CG force field or water model, GROMACS Wizard supports using your own solvents. You can apply this same spacing tweak even with custom setups. You’ll just need to provide your own structure and topology files—SAMSON will handle loading them accordingly.
Conclusion
It only takes a few seconds, but increasing the default solvent spacing can save you hours of troubleshooting down the line. Setting up your periodic box correctly with the right van der Waals distance results in better-packed systems and more stable coarse-grained simulations.
To learn more about how to set up your entire CG system and streamline MD simulations in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.