When preparing coarse-grained molecular dynamics (MD) simulations with GROMACS, many users encounter an unexpected obstacle: solvent molecules too close to the solute. This typically results in unrealistic overlaps and density artifacts that force them to redo the setup or troubleshoot simulations. If you’ve faced unusual starting structures or failed energy minimizations, there’s a good chance solvent packing is the issue.
Fortunately, if you’re using SAMSON’s GROMACS Wizard with MARTINI coarse-grained models, there’s a straightforward way to avoid solvent clashes by adjusting a key parameter during system preparation: the van der Waals distance.
Why Does This Happen?
Unlike atomistic models, coarse-grained beads represent multiple atoms. For example, a single MARTINI water bead stands for four water molecules. However, GROMACS still uses a default van der Waals contact distance of 0.105 nm, which is fine for atomistic systems but too small for coarse-grained ones. This leads to solvent molecules being placed too close to each other and to the solute, resulting in structural clashes.
How to Fix It in SAMSON
When you’re in the Prepare tab of the GROMACS Wizard and you check the Add solvent option, click the gear icon 
to access the solvent settings. In the pop-up window, increase the van der Waals distance to something more appropriate for coarse-grained simulations – 0.21 nm is a good default. This modification ensures better packing and minimizes unwanted overlaps.
Here’s how the process looks inside SAMSON:
And here’s the solvent options window with the adjustable van der Waals distance:
Best Practices
- Always verify that the system was generated using a compatible coarse-grained force field, like MARTINI v.3.0.0.
- Make sure to adjust the solute-box distance to maintain at least 1 nm between solute and the box edge.
- Changing the box type to Rhombic dodecahedron can save computational resources while keeping symmetry.
- Only add ions after solvent is added, since ions replace solvent beads.
Conclusion
Solvent clashes are a common stumbling block in CG MD simulations, but with SAMSON’s GROMACS Wizard, they’re easy to avoid. If you take a few seconds to optimize the van der Waals distance during solvent addition, your system will be much more reliable and ready for productive simulations.
To learn more about coarse-grained system preparation in SAMSON, visit the full tutorial at: 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.