The small distance setting that can make or break coarse-grained solvation

Preparing a coarse-grained system for molecular dynamics can look straightforward: load the model, add water, and move on to ions and simulation. But a setting that is reasonable for an atomistic system may be too small for coarse-grained beads. The result can be an awkwardly packed solvent environment or clashes around the solute.

For MARTINI coarse-grained systems, one important detail is the van der Waals distance used during solvation. GROMACS does not have van der Waals distances defined for every coarse-grained model. When it falls back to the default value of 0.105 nm, that distance may be too close for coarse-grained beads. A Martini water bead represents four water molecules, so it is not equivalent to placing a single atom-sized water particle at the same spacing.

The GROMACS Wizard tutorial recommends increasing the default van der Waals distance when adding solvent—for example, to 0.21 nm. Treat this as the documented example, rather than a universal value for every model. Other solvent options can remain at their defaults unless your setup calls for a custom solvent model.

A preparation workflow that avoids common snags

1. Keep the input files together. Start with a valid coarse-grained model. If it was generated with Martinize2, keep the generated structure and topology files in the same folder. The folder should contain files such as *_CG.pdb and *_CG.top, along with any relevant topology include files.
2. Load the model to establish the box. In the GROMACS Wizard Prepare tab, set the system source to Folder, browse to the model folder, and check the detected PDB, TOP, and ITP files. Load the PDB file; this is the step that computes the periodic box for the system.
3. Check the force field before preparing. For a model generated by the documented Martinize2 workflow, confirm that the force field is martini_v.3.0.0 and that the default Martini water model is selected. If your model uses a different coarse-grained force field, provide that force field rather than assuming the MARTINI setting is appropriate.
4. Set solvent and box options deliberately. If you want to solvate the system, enable Add solvent and open its options. Increase the van der Waals distance as described above. Also review the periodic box: the tutorial notes that the solute-box distance should be at least 1 nm to ensure the minimum distance between periodic images. A rhombic dodecahedron is another available unit-cell choice.
5. Add ions only as part of a solvated setup. Choose ions to neutralize the system, and specify additional salt concentration if needed. The Add solvent option must be enabled because ions are added by replacing solvent molecules.

After selecting Prepare, you can load and inspect the resulting structure. Once it is ready, move to the Minimize tab and use the auto-fill button to take the previous step’s results as the input structure. Advanced preprocessing options also show position restraints detected from the topology. With Martinize2, restraint records can be generated separately for molecules; check the relevant definitions rather than assuming every molecule has the same restraint setup.

The broader lesson is to check the scale of the model before accepting defaults. Coarse-grained beads represent groups of atoms or molecules, so a distance intended for atomistic particles may not be suitable. A quick review of the solvent distance, box, force field, and ion settings can help prevent avoidable preparation problems before minimization and equilibration.

For the full workflow and screenshots, see the GROMACS Wizard coarse-grained systems tutorial.

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