When preparing coarse-grained (CG) molecular systems for molecular dynamics (MD) simulations, one crucial step is the addition of ions. This step ensures charge neutrality and mimics physiological conditions. However, it’s easy to encounter unexpected issues—especially when working with CG models—if a few important details are overlooked. If you’ve ever puzzled over non-neutralized systems or simulation crashes, this post is for you.
The setup challenge
In CG systems, solvent molecules are simplified. A single Martini water bead, for instance, represents four actual water molecules. As a result, van der Waals distances and solvent volumes don’t behave as intuitively as in atomistic detail. This poses a challenge when adding ions because GROMACS typically replaces solvent molecules with ions to achieve neutrality or the desired salt concentration.
Step-by-step: reliable ion insertion
Let’s break down the steps users should follow in SAMSON’s GROMACS Wizard to avoid ion insertion issues:
- Enable solvent addition first: Ion addition depends on solvent presence as ions replace solvent molecules. Ensure you’ve selected Add solvent before activating the ion insertion step.
- Adjust the van der Waals distance: By default, GROMACS uses 0.105 nm as the van der Waals threshold, which is often too small for CG systems, leading to bead overlaps or low-density solvation. Open the solvent settings and increase this distance to around 0.21 nm. This will reduce clashes and improve density.
- Customize box geometry: You can choose a more efficient unit cell type, like a Rhombic dodecahedron, to save computational resources and maintain symmetric boundaries.
- Select ion types and salt concentration: Back in the main panel, choose the types of positive and negative ions (such as Na+ and Cl-) and set the salt concentration. The system will be automatically neutralized unless you specify otherwise.
Why correctness matters
Incorrectly added ions can cause your simulation to fail at the energy minimization or equilibration stages. Sometimes, the system reports unphysical densities or unexpected net charges. Double-checking that solvent is present, van der Waals distances are adapted to CG beads, and ion placement parameters are sensible helps prevent these problems early.
Bonus tip: inspect results before moving on
After the Prepare step, always review the prepared structure visually. SAMSON colorizes ion beads using the classic CPK color scheme, so you can easily spot them in your solvated system.
Spending a few minutes tweaking parameters before pressing Prepare can save you hours chasing down odd results later in your workflow.
For more detailed guidance, explore the full documentation page at 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.