The Small Distance That Can Disrupt a Coarse-Grained Solvation Setup

Preparing a coarse-grained model for molecular dynamics can look straightforward: load the structure, add water, add ions, and prepare the simulation. But a default setting that works for an atomistic system may be too small for coarse-grained beads. In GROMACS Wizard, the van der Waals distance used during solvation is one setting worth checking before you prepare the system.

This matters especially for MARTINI models, where one water bead represents four water molecules. The GROMACS Wizard tutorial notes that GROMACS may use a default van der Waals distance of 0.105 nm because distances are not defined for the coarse-grained model. That value may be too close for coarse-grained beads. Increasing it—for example, to 0.21 nm—helps avoid clashes and supports proper solvent density.

A practical preparation sequence

Start with a valid coarse-grained model and keep its structure and topology files together. If the model came from Martinize2, choose the output folder containing files such as *_CG.pdb and *_CG.top, along with the related topology files.

  1. Open GROMACS Wizard and go to Prepare. Under Set system, choose Folder, browse to the model’s folder, and check that the expected PDB, TOP, and ITP files are detected.
  2. Load the detected PDB file. This loads the structure and computes its periodic box.
  3. For a MARTINI v.3.0.0 model generated with Martinize2, check that the force field is set to martini_v.3.0.0. The wizard switches to this force field automatically for such a model, but it is still worth verifying. If you use a different coarse-grained force field, you need to provide it.
  4. If you want solvent, enable Add solvent and open its options. Increase the default van der Waals distance to a suitable coarse-grained value—for example, 0.21 nm—and leave other options at their defaults unless your setup requires otherwise.

Solvent options for a coarse-grained system

Check the box and ions, too

Review the periodic box before preparing. You can adjust the solute-box distance; the tutorial advises keeping it at least 1 nm to ensure the minimum distance between periodic images. A rhombic dodecahedron is another option: it is a small, regular space-filling unit cell.

If you need to neutralize the system or add salt, select the positive and negative ions and set any additional salt parameters. One easy-to-miss dependency: ions are added by replacing solvent molecules, so Add solvent must be enabled when you configure ions.

A computed periodic box around the coarse-grained structure

Once the settings are in place, click Prepare. You can load and inspect the prepared structure, or continue to minimization. If you inspect it, the document also includes GROMACS index groups that you can double-click to select their associated structures.

A quick preflight checklist

  • Are the structure and topology files together and detected?
  • Is the intended coarse-grained force field selected?
  • Has the solvent van der Waals distance been increased from the default when needed?
  • Is the box distance at least 1 nm?
  • If adding ions, is solvent enabled?

These checks help catch preparation choices that are easy to overlook before moving on to minimization and equilibration. For the full workflow and further details, see the GROMACS Wizard coarse-grained systems tutorial.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

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