When preparing coarse-grained (CG) molecular systems using GROMACS, one frequent source of frustration for modelers is unexpected initial clashes or abnormal solvent behavior during equilibration. If you’ve been there — puzzled by poor density or unstable simulations — the issue might stem from how solvent molecules are added in the CG context. In this post, we look at how SAMSON’s GROMACS Wizard helps avoid a common pitfall: inadequate van der Waals spacing when solvating CG systems.
Why solvating CG systems requires extra care
In atomistic simulations, van der Waals (vdW) distances are well-defined per atom type. But in coarse-grained systems — where one bead may represent several atoms or even molecules — these parameters are more ambiguous. For example, in the MARTINI force field, one water bead typically represents four water molecules, making the default vdW overlap check (at 0.105 nm) too tight. This can result in solvent molecules being placed too close, causing unrealistically high local densities or structural instabilities in MD.
How SAMSON handles this
The GROMACS Wizard in SAMSON includes a step-by-step interface to solvate systems and addresses this issue with customizable options.
Here’s how:
- After loading your CG model (e.g., from Martinize2), navigate to the Prepare tab and check Add solvent.
- Click the gear icon
next to this option to open advanced parameters. - In the popup window, increase the default vdW distance cutoff from 0.105 nm to about 0.21 nm.
This adjustment ensures that solvent beads are positioned at a more realistic distance in accordance with the Martini model, avoiding structural overlap that GROMACS would not otherwise prevent for such CG beads.
When and why to adjust further
The 0.21 nm recommendation works for MARTINI water, but if you’re using a custom solvent model with different bead sizes or solvation shell assumptions, you may need to tweak this value accordingly. The key principle: ensure adequate spacing for coarse representations.
Bonus: Adding ions
The solvent options are also a prerequisite for ion placement. GROMACS adds ions by replacing solvent molecules, so this vdW spacing trick ensures that those molecules are well-distributed, giving you consistent ionization without unintentional clustering.
Conclusion
Whether you’re just getting started with CG MD simulations or refining a complex system, a small tweak in solvent vdW parameters can make a big difference. SAMSON’s GROMACS Wizard makes this adjustment accessible and integrated into your preparation workflow.
Learn more from the original documentation page: 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.