When preparing a coarse-grained (CG) molecular system for simulations, a common frustration is the appearance of solvent clashes that can cause a simulation to fail. These clashes often originate during the solvation stage, especially for CG models using the MARTINI force field. Fortunately, the GROMACS Wizard in SAMSON offers a clear solution to avoid these issues, without requiring you to manually write complex input files or scripts.
Understanding the core issue ❗
In all-atom simulations, GROMACS uses van der Waals (vdW) parameters to determine minimal allowed distances between molecules during solvation. For coarse-grained models, however, these vdW distances are not always defined or appropriate. For example, MARTINI water beads represent multiple water molecules—typically four—so the default vdW threshold (0.105 nm) used by GROMACS may be too low, resulting in overlapping beads.
How to prevent clashes in SAMSON’s GROMACS Wizard
To solve this, the CG-specific tutorial for GROMACS Wizard suggests increasing the vdW distance used when adding solvent. Here’s how:
- In the Prepare tab of the GROMACS Wizard, check the Add solvent box.
- Click on the gear icon (
) next to the solvent options. - In the pop-up window, adjust the van der Waals distance to a safer value—recommendations suggest 0.21 nm as a conservative default. This prevents unrealistic overlaps.
This one step can prevent hours of debugging broken coordinate files or unexplained crashes in minimization or equilibration stages.
Why this matters
If you’re modeling biomolecular systems using MARTINI or other CG force fields, you’re likely doing so for larger systems or longer time scales. Wasting computation on broken systems is costly. This small change has a big impact: your system remains physically reasonable, and your workflow continues smoothly from solvation to energy minimization.
Optional: Provide your own solvent model
If you are using a custom CG solvent model, the GROMACS Wizard also allows you to supply your own. For this, see the section Using a custom solvent model in the Prepare tutorial.
Conclusion
A small tweak—changing the van der Waals distance when adding solvent—can dramatically improve the stability of your CG system preparation. Whether you’re studying large protein complexes or membranes with the MARTINI force field, this adjustment ensures smoother preparation and simulation steps.
To learn more about preparing coarse-grained systems in GROMACS Wizard, visit the full tutorial: GROMACS Wizard – Coarse-grained systems.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.