One of the common frustrations when working with coarse-grained (CG) molecular systems—especially those based on the MARTINI force field—is the appearance of unexpected solvent clashes. This often happens during system solvation using GROMACS default settings, which aren’t tailored for coarse-grained models. If you’ve had your minimization or equilibration jobs fail due to high energy or instability, this post might help.
In CG models, each water bead represents multiple water molecules (usually 4), and the spatial scale is different from that of all-atom systems. However, GROMACS doesn’t automatically adjust for this when solvating, and defaults to using a van der Waals (vdW) distance of 0.105 nm. For CG beads, this can cause solvent molecules to be placed too closely, leading to inaccurate solvent densities or immediate structural deformation on MD start.
Using SAMSON’s GROMACS Wizard to Fix This
The GROMACS Wizard in SAMSON comes with built-in awareness of coarse-grained setups, including force fields like MARTINI v3.0.0. When you add solvent in the Prepare tab, a gear icon next to the Add solvent checkbox gives you access to solvent parameters.
What to Change
Click the gear icon to open solvent options. Then:
- Increase the van der Waals distance from
0.105 nmto 0.21 nm. - Keep the other settings as default unless you have specific requirements.
This spacing better reflects the typical distance between MARTINI CG beads and helps avoid packing solvent molecules too tightly, which would otherwise result in unrealistic solvent densities or structural instabilities later during simulation.
This simple adjustment can significantly improve the quality of the prepared system and save you from debugging instability issues that are hard to trace back to their source.
Additional Notes
- If you’re using a custom coarse-grained solvent model, SAMSON allows you to load it as well. See this section in the documentation for more info.
- SAMSON automatically sets the force field to MARTINI v3.0.0 when it detects a MARTINI topology, but do verify this in the force field panel.
Small Change, Big Difference
Adjusting the van der Waals distance during solvation might seem like a minor tweak, but it’s an important one that directly addresses how GROMACS treats CG models. Without it, you risk solvent overlaps that could derail your MD simulations down the line. The SAMSON GROMACS Wizard provides a straightforward way to make this adjustment without editing configuration files manually.
To learn more about preparing coarse-grained systems using the GROMACS Wizard in SAMSON, visit the full tutorial documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.