Setting up a coarse-grained (CG) system for molecular dynamics simulations can save time and computational resources, but comes with its own challenges. One such challenge — often overlooked by beginners — is related to how solvent molecules are added to a system. Incorrect solvation can lead to overlapping particles and unstable simulations.
If you’re using the Martini force field and preparing systems in the GROMACS Wizard inside SAMSON, there’s a simple but essential step to make your simulations cleaner and more robust.
What Goes Wrong During Solvation?
When you add solvent molecules to your CG system, GROMACS uses van der Waals (vdW) distances to prevent them from overlapping with existing atoms. However, for coarse-grained beads — like those in the Martini model — GROMACS doesn’t define vdW distances. Instead, it defaults to 0.105 nm, which is appropriate for atomistic water, but too small for coarse-grained beads where a single water bead might represent 4 water molecules.
This can lead to unrealistically packed or clashing waters — a problem that’s tough to detect visually, but can crash your simulations or produce artifacts.
A Simple and Effective Solution
GROMACS Wizard offers a clean interface to address this. Here’s how to adjust the solvation step correctly:
- In the Prepare tab, activate the Add solvent option.
- Click the gear icon next to the option to open the solvation options window.
- Set the van der Waals distance to a safer value such as
0.21 nm. This ensures that solvent molecules are placed with an appropriate buffer zone around CG beads. - Click OK, and continue preparing your system as usual.
This one tweak can prevent unnecessary debugging headaches later. Water placement in coarse-grained systems is non-trivial, and taking a few seconds to configure this properly is well worth the effort.
Optional: Custom Solvent Models
If you have a specific solvent model you’d like to use — for example, modified coarse-grained waters or other environments — GROMACS Wizard also supports importing custom solvent topologies. You can learn more about this in the custom solvent model section of the documentation.
Takeaway
When preparing CG systems in SAMSON’s GROMACS Wizard:
- Never rely on the default van der Waals distance during solvation.
- Use
0.21 nmor another appropriate value to reflect CG bead sizes. - This tweak avoids solvent overlap and improves simulation stability.
Want more tips or ready to follow the full tutorial? Explore the complete documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.