When setting up molecular dynamics (MD) simulations using coarse-grained (CG) models, one recurring issue modelers face is improper solvation: water molecules overlapping with solute atoms or each other. This can happen easily when using default settings that are not tailored for CG topologies, and it often causes failed minimizations or unrealistic starting configurations. In this post, we’ll walk through how to avoid such clashes using the Add solvent options available in the GROMACS Wizard in SAMSON.
Coarse-grained systems, such as those based on the MARTINI force field, simplify molecular structures by grouping several atoms (e.g., four water molecules) into one bead. However, this simplification introduces specific constraints regarding spacing—standard atomic-scale van der Waals distances are just not appropriate when each bead represents much larger molecular volume.
Understanding the Solvent Clash Problem
In atomic-detail models, van der Waals (vdW) radii are clearly defined and used to calculate non-overlapping solvent placements. In coarse-grained systems, these vdW values are often absent or too small for realistic spacing since the beads represent multiple atoms. If you use GROMACS Wizard with the default vdW threshold (0.105 nm), solvent beads can end up unrealistically close, causing high-energy configurations and unstable simulations.
The solution? Manually adjusting the solvent placement parameters before solvation.
How to Adjust Solvation Parameters
Once you’ve loaded a CG system in GROMACS Wizard and reached the Add solvent step, click the small gear icon to open advanced solvent settings:
In the launcher, increase the van der Waals distance from the default 0.105 nm to a more appropriate CG-safe value. For the MARTINI model, a good starting point is 0.21 nm:
This simple change ensures solvent beads are placed with appropriate spacing for CG simulations, lowering the risk of starting clashes and ultimately reducing the chance of failing the minimization step.
Tips for Better Solvation
- Always apply this solvent adjustment before adding ions—ions are placed by replacing solvent molecules.
- Prefer using the MARTINI solvent model shipped with the Wizard for compatibility.
- You can also load your custom CG solvent model if you have specific simulation requirements.
- Visually inspect the solvation layer after applying these settings by loading the prepared system—SAMSON colorizes water beads in blue for easier identification.
A well-solvated and non-clashing CG system ensures the success of subsequent steps such as energy minimization and equilibration. This preparation tip might seem small—but it can save hours of troubleshooting later.
Learn more and follow the full tutorial on preparing coarse-grained systems using GROMACS Wizard: documentation.samson-connect.net
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.