Avoiding Pitfalls in Coarse-Grained MD: Setting Up Solvents and Ions Correctly

One of the most overlooked yet crucial steps in preparing coarse-grained molecular dynamics (MD) simulations is solvent and ion setup. If coarse-grained (CG) models are incorrectly solvated or ionized, simulations often produce unrealistic results—or fail entirely.

This blog post focuses on avoiding common pitfalls in the solvation and ion placement step when preparing coarse-grained systems using the GROMACS Wizard in SAMSON. It also introduces a few tips that can save you hours of debugging simulation errors.

Why Solvent and Ions Matter in CG MD

In coarse-grained representations like the MARTINI force field, several atoms are grouped into larger beads. For instance, one water bead typically represents four actual water molecules. As a result, default atomic-scale values for parameters like van der Waals (vdW) distances no longer apply directly.

This becomes particularly important when solvents are added automatically: unless corrected, vdW clashes between CG beads can result in an inaccurate or unstable system.

How to Solvate Properly in GROMACS Wizard

To correctly solvate your CG model in GROMACS Wizard:

  1. Check the Add solvent option.
  2. Click the gear icon next to it to open solvent options.
  3. In the pop-up window, increase the default van der Waals distance from 0.105 nm to something like 0.21 nm.

Doing so prevents bead overlaps and ensures proper density. Beads that are too close will cause atom clashes. A properly spaced system is computationally stable from the get-go.

Solvent options

Adding Ions the Right Way

Ions help you neutralize your system or replicate biological ion concentrations. Here’s what to keep in mind:

  1. You must add solvent before adding ions, since ions replace solvent molecules.
  2. Select the types of ions (positive/negative) needed for neutralization.
  3. To add a specific salt concentration, enable the option and input the desired molarity.

Add ions - Salt concentration

These steps ensure not only electroneutrality but also a realistic ionic environment.

When Using a Custom Solvent Model

If you’re not using the default MARTINI water model, you can also provide a custom CG solvent. Just make sure to match it with the correct topology and force field. Guidance is provided in the GROMACS Wizard documentation for custom solvent models under this section.

Final Checklist for Solvent and Ion Setup

  • Set van der Waals distance to at least 0.21 nm for MARTINI water beads.
  • Always check solvent options after enabling the solvate checkbox.
  • Add ions after enabling solvent addition.
  • Double-check that the correct force field (e.g., martini_v.3.0.0) is selected.

Getting these settings right helps ensure a smooth flow as you move into energy minimization, equilibration, and production MD runs.

Want to learn more? See the full documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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