Preparing a coarse-grained (CG) system for molecular dynamics (MD) simulations can often be frustrating when solvent models behave unexpectedly. One common issue many molecular modelers face is improper solvation due to van der Waals (vdW) clash errors or insufficient solvent density when working with CG systems, especially with the MARTINI force field.
Why does this happen? Traditional force fields come with vdW parameters that guide solvent placement, but CG force fields—like MARTINI—do not have these defined for all bead types. As a result, simulation engines like GROMACS default to a minimal distance of 0.105 nm, which may be too small when each CG bead represents multiple atoms or molecules (for example, one MARTINI water bead represents four real water molecules).
This short blog post explains how to correctly solvate CG systems using the GROMACS Wizard in SAMSON, avoiding unwanted artifacts and simulation instabilities.
Solvating CG Systems the Right Way
In the Prepare tab of the GROMACS Wizard, after loading the CG system (for instance, one generated with Martinize2), you can choose to add solvent by checking the corresponding checkbox. Here’s where attention is required.
Click on the gear icon 
next to “Add solvent” to fine-tune solvent parameters. Increase the default vdW distance to ensure beads are placed in physically reasonable positions and not too close to each other. The MARTINI CG community commonly uses a minimum value of around 0.21 nm. This helps reduce artifact formation and ensures that the density of the solvent more accurately reflects realistic conditions.
Leave the rest of the options at default if you’re unsure—adjusting the vdW distance is typically sufficient for most solvent setups. If you want even greater control, SAMSON also supports using a custom CG solvent model.
Why This Matters
Skipping this step may result in your system being solvated with overlapping beads, leading to force spikes and crashes during simulation. It can also yield incorrect solvent densities, affecting the thermodynamics and structural behavior of your simulation. Correct solvation is especially important when working with complex systems or aiming to measure physical properties such as solvation free energies or ion distributions.
After adjusting the solvent settings, you can proceed to add ions. Remember: GROMACS adds ions by replacing solvent molecules, meaning the solvent must be added before ion addition is possible. You can opt to neutralize the system or simulate physiological environments by specifying a salt concentration.
This step-by-step approach ensures that your CG MD simulation starts with physically sensible coordinates, a critical condition for meaningful trajectory data and accurate results.
To learn more about CG system preparation in the GROMACS Wizard, including box setup and minimization, visit the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.