Adding Ions in Coarse-Grained MD: A Small Step That Can Complicate Everything

When preparing coarse-grained (CG) molecular systems for simulations in GROMACS, one often focuses heavily on force fields, solvation, and the periodic box—but there’s a crucial final step before minimization that can make or break a simulation: adding ions. 🧪

Adding ions is important both for neutralizing the system and for mimicking physiological environments through salt concentrations. However, in CG simulations—especially using the MARTINI force field—this step requires some additional care due to the simplified nature of the system. This post walks you through how to correctly neutralize your CG system and optionally add salt when using the GROMACS Wizard in SAMSON.

Why adding ions matters

In CG molecular dynamics (MD), each bead represents a group of atoms. For MARTINI models, each water bead represents ~4 water molecules. This makes electrostatic interactions quite sensitive to the number and positioning of ions—errors here can lead to unrealistic behavior or even simulation crashes.

Moreover, ions in CG systems typically replace solvent beads, which means you must solvate the system before attempting to add ions.

Step-by-step: Neutralization and salt in GROMACS Wizard

  1. After solvation, check the option to “Add ions” in the Prepare tab.
  2. Choose the ions you want to add. You can select from typical cations and anions (e.g., Na+, Cl–).
  3. To neutralize the charge of the system, simply check the “Neutralize” option. GROMACS Wizard will calculate the net charge and add the appropriate number of ions.
  4. Optionally, if you want to reflect a specific ionic strength (e.g., 0.15 M NaCl), you can manually set the desired salt concentration.
  5. Click the Prepare button to run the ion addition command. If all goes well, water beads will be replaced by the ions you’ve specified.

Add ions - Salt concentration

Best practices to avoid issues

  • Always increase the van der Waals (vdW) distance before solvation to avoid overlap: around 0.21 nm is recommended for CG systems.
  • If ions are not added correctly, double-check that the system was solvated and that a topology file (.top) is present with appropriate ion parameters.
  • Pay attention to the force field: GROMACS Wizard automatically selects martini_v.3.0.0 if your system was generated via Martinize2, but if you’re using a custom CG force field, ensure the ions are defined there.

A visual cue

Once the system is loaded, SAMSON will uniquely color CG water beads in blue and ions using CPK colors to help users visually confirm that ions have been added correctly.

While adding ions might seem like a minor task, doing it wrong can significantly affect the realism and stability of your CG molecular dynamics simulations. The GROMACS Wizard simplifies this process for MARTINI systems, but attention to detail—especially with vdW distance and solvation—is key.

To learn more about preparing CG systems in GROMACS Wizard, visit the original documentation page: GROMACS Wizard – Coarse-grained systems

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

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