When preparing coarse-grained (CG) models for molecular dynamics (MD) simulations in GROMACS using the MARTINI force field, one common source of simulation instability is improper solvation. Users often follow the traditional pipeline for all-atom models, only to find that water molecules overlap unrealistically with solute beads, leading to artifacts in energy minimization or crashes later on.
In the SAMSON GROMACS Wizard, there is a specific step dedicated to helping you avoid this issue. Here’s a deeper look at why it occurs and how you can address it using SAMSON’s intuitive interface.
Why Van der Waals Distance Matters for CG Models
Unlike all-atom models, coarse-grained beads in the MARTINI force field represent groups of atoms. For example, a single water bead models four water molecules. GROMACS, by default, uses a small van der Waals exclusion distance (0.105 nm). This is often too close for CG particles, causing solvent molecules to overlap with solute beads.
To address this, the GROMACS Wizard in SAMSON enables adjustment of the van der Waals distance during solvation. By increasing this value (e.g., to 0.21 nm), you prevent unwanted molecular overlaps and ensure a more physically realistic starting configuration.
How to Adjust the Solvation Parameters
- Once you have prepared your CG system in the GROMACS Wizard (e.g., loaded a martini_v.3.0.0 system generated via Martinize2), go to the Prepare tab.
- Check the box labeled Add solvent.
- Click on the gear icon next to it to open advanced solvent options.
- In the pop-up window, find and increase the van der Waals distance to at least 0.21 nm.
- Click OK, and continue with box resizing or ion addition if needed, then click Prepare.
This modest change makes a significant difference, especially in large CG systems where solvent density and overlap directly affect MD stability and simulation results. It’s a small but critical step that many overlook, especially if they use automated workflows or assume solvation defaults are universally safe.
Tip: Custom Solvent Models
If you are using a non-default MARTINI CG solvent, you can also load your custom solvent definitions into GROMACS Wizard. For this, refer to the section on Using a custom solvent model.
For more details and step-by-step visuals, visit the full tutorial on coarse-grained systems with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.