Why Your Coarse-Grained MD May Be Unstable (And How Ions Can Help)

When preparing coarse-grained (CG) molecular dynamics (MD) systems—especially with force fields like MARTINI—you might run into unexpected instabilities during equilibration or production runs. A common underlying cause? Forgetting to neutralize the system or set the proper ionic conditions. Fortunately, GROMACS Wizard in SAMSON includes a step to easily add ions to your system—and doing it correctly can save hours of troubleshooting later on.

Why charge neutrality matters

Even if your visual inspection shows a “valid” structure, an unbalanced net charge can cause energy minimization to fail, or lead to unrealistic forces during MD simulations. Coarse-grained systems exaggerate this further because their simplified representation amplifies electrostatic inconsistencies.

To address this, ions like Na+ or Cl− must sometimes be added to balance the system or mimic physiological salt concentrations. GROMACS does this by replacing solvent molecules, assuming your system is already solvated.

How SAMSON helps

During the Prepare step using GROMACS Wizard in SAMSON, simply:

  1. Ensure your CG system is correctly loaded and solvated.
  2. Check the option Neutralize / Add additional ions.
  3. Choose the types of positive and negative ions (e.g., Na+ and Cl−).
  4. Optionally, set a specific salt concentration (e.g., 0.15 mol/L for physiological conditions).

Add ions - Salt concentration

What’s often overlooked

Note

Ions are only added if the system is already solvated. This makes sense, as ions replace water molecules. So, if you skip the Add solvent step, the ion insertion won’t be applied—even if you check the box.

Tips for stable CG simulations

  • Set the solute-box distance to at least 1 nm to minimize artificial interactions with periodic images.
  • Use a unit cell type like Rhombic dodecahedron to save on computational load while maintaining simulation quality.
  • Match your force field and solvent models (SAMSON auto-selects martini_v.3.0.0 if you used Martinize2).

Adding ions might feel like a footnote in MD preparation, but it’s a vital one. Especially in coarse-grained simulations, where the implicit assumptions of the model make system neutrality and realistic ionic strength even more important. GROMACS Wizard in SAMSON brings structure and clarity to this step without requiring command-line work or manual edits to topology files.

To learn more about CG system preparation with GROMACS Wizard in SAMSON, check out the full tutorial.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

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