One of the trickiest steps when setting up a coarse-grained (CG) system for molecular dynamics (MD) simulations is solvation — especially when using popular CG force fields like Martini. A common frustration among researchers is finding out, only after running a simulation, that solvent beads are overlapping or behaving oddly. This post walks you through an important but often-overlooked detail when solvating CG systems with the SAMSON GROMACS Wizard.
What Makes Solvating CG Systems Different?
Unlike all-atom systems, CG models like those that use Martini beads compress several atoms into one pseudo-atom or bead. For example, a single Martini water bead represents four water molecules. That has various implications, but one immediate technical one is: the default van der Waals (vdW) distance will likely be too small.
GROMACS does not natively define vdW distances for CG beads, and so it defaults to using 0.105 nm — a number that makes sense for atoms, but not quite for beads that represent four water molecules. If you don’t override it, your solvent beads could end up too close to solute beads or even to each other, causing unrealistic densities and making equilibration fail or yield misleading results.
How to Properly Solvate in GROMACS Wizard
The solvation step in SAMSON’s GROMACS Wizard provides an easy-to-access window for configuring solvent options. The key setting to look for is the van der Waals distance. Here’s your action plan:
- After choosing to Add solvent in the Prepare step, click the gear icon
next to the checkbox. This opens a window with solvation options. - Locate the van der Waals distance parameter and increase it to at least
0.21 nm. This doubles the default and is more appropriate for Martini water beads. - Keep other parameters unchanged unless you know they need customization for your system.
A correct vdW setting ensures proper density of the solvent and helps prevent overlapping beads — increasing the chances your system passes energy minimization and runs stably.
Optional: Use a Custom Solvent Model
SAMSON also lets you provide a custom CG solvent model if you’re using force fields other than Martini or tailoring your system to a specific need. For that, check the detailed instructions on using a custom solvent.
Final Note
Solvation is one of those things that “just works” — until it doesn’t. With CG systems, default settings don’t always apply. Making a small tweak like adjusting the vdW distance can save hours of troubleshooting and confusing output later. SAMSON’s GROMACS Wizard gives you direct control over these critical details — awareness of them is all you need.
To learn more and go through the full tutorial step-by-step, visit the original page on GROMACS Wizard – Coarse-Grained Systems.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and access the GROMACS Wizard and Martinize2 Extensions at samson-connect.net.