When preparing coarse-grained (CG) molecular systems for simulation with GROMACS, one of the crucial—but often overlooked—steps is setting the proper van der Waals distance for solvation. If this value is left unchanged, the solvent might clash with solute beads, leading to degraded models or unexpected behaviors in MD simulations. 🧪
This situation often arises when modeling with the GROMACS Wizard Extension in SAMSON, especially when using automatically generated CG structures from Martinize2, which supports the MARTINI v.3.0.0 force field.
Why this matters
In CG models like MARTINI, water beads represent multiple actual water molecules—typically four. When running solvation in GROMACS, the software resorts to default van der Waals distance values if none are specified for CG beads. The default (0.105 nm) is appropriate for all-atom models but often too low for CG systems.
This can result in water beads being placed too close to other CG beads, causing initial strain in the model and potentially unphysical interactions during simulation.
How to fix it in SAMSON’s GROMACS Wizard
Here is how you can avoid this issue directly in the GROMACS Wizard interface:
- After loading your CG model from a folder (e.g., output from Martinize2), ensure your system is loaded properly to compute the periodic box.
- In the Prepare tab, check the Add solvent box and click on the gear icon
to adjust options. - In the pop-up dialog, look for the van der Waals distance setting and increase it from the default
0.105 nmto at least0.21 nm. - Confirm your solvent density and adjust any other relevant parameters before proceeding.
This simple adjustment can drastically improve the quality and stability of your CG simulations. The image below shows the solvent options window with the recommended value.
Why 0.21 nm?
The MARTINI model does not define standard van der Waals distances for individual beads in the way atomistic force fields do. Instead, the sizes are implicit in the bead types and how they interact. A value of 0.21 nm is a well-tested approximation to ensure solvent molecules are placed with appropriate separation, reflecting the effective size of these CG beads.
What if you use a custom solvent model?
SAMSON also lets you use custom solvent models. When doing so, make sure you also adjust the van der Waals distance accordingly, based on how your particular model defines interactions between solvent and solute beads.
Wrapping up
Solvent settings in coarse-grained simulations deserve careful attention. A quick change in just one numerical parameter—van der Waals distance—can save hours of failed simulations and make your results more reliable. Whether you’re new to CG modeling or fine-tuning a complex biomolecular system, this is a step worth bookmarking.
To learn more, follow the full tutorial here:
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.