Avoiding Common Pitfalls When Adding Ions to Coarse-Grained Systems in GROMACS Wizard

One of the subtle yet critical steps when setting up molecular dynamics (MD) simulations with coarse-grained (CG) models is ion addition. If not handled properly, the system can become unbalanced or lead to non-physical behavior during simulation. Fortunately, the GROMACS Wizard Extension for SAMSON provides a streamlined process for adding ions to CG systems, with some important nuances you should be aware of.

Let’s explore how to properly neutralize your system and add ions when working with MARTINI-based models in GROMACS Wizard.

Why Ion Addition Can Be Tricky for CG Models

Unlike all-atom models, CG models like MARTINI represent several atoms with large beads. Water beads, for example, each represent four water molecules. This changes the way ions interact with the solvent, which matters when the simulation involves electrostatics or membrane systems.

Moreover, GROMACS does not store van der Waals distances for CG beads. That means that defaults might be too small, can cause overlaps, or lead to unrealistic densities unless we guide the system with proper parameters.

Step-by-Step: Adding Ions in GROMACS Wizard

  1. Enable Solvent First: You need to enable solvent addition because ions are added by replacing solvent molecules. Make sure “Add solvent” is checked.
  2. Open Solvent Options: Click the gear icon next to “Add solvent.” Increase the van der Waals distance to at least 0.21 nm to avoid bead clashes. This is particularly important for MARTINI water beads.
    Solvent options
  3. Adjust the Periodic Box: Ensure the solute-box distance is at least 1 nm and consider using the Rhombic dodecahedron unit cell to reduce the number of required solvent molecules while maintaining space filling.
    Computed periodic box
  4. Choose Ions: After solvent is configured, scroll down and check the option to add ions. You can either let GROMACS Wizard neutralize the system or manually provide a salt concentration. Both actions are done by replacing water beads.
    Add ions - Salt concentration

Pro Tip: Avoid Overshooting Ion Concentration

Be conscious of the concentration-to-box-size relationship. For coarse-grained models with smaller system sizes, even modest salt concentrations can translate to a significant number of ions. Use SAMSON’s interactive document view to visually inspect ion placement after system preparation.

Once ions are added, you can proceed to energy minimization and equilibration. The Wizard will auto-populate files from the preparation step and apply any POSRES defines from the topology files to ensure stable relaxation of your system.

Takeaway

Ion addition in CG systems is more than a click-through step. It requires small yet essential tweaks to mimic realistic biological conditions. GROMACS Wizard’s integration in SAMSON makes this process transparent and repeatable, especially for MARTINI-based modeling.

To learn more about the full CG preparation pipeline, including ion addition, 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 at samson-connect.net.

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