A coarse-grained model can look ready for simulation and still run into trouble at the preparation stage: solvent beads may be placed too close to the model. This is easy to miss if you are used to atomistic workflows, because coarse-grained beads represent groups of atoms and need more space than a single water molecule.
In GROMACS Wizard, the default van der Waals distance used for adding solvent may be too small for a coarse-grained system. The documentation explains why: GROMACS does not have van der Waals distances defined for coarse-grained models in this case, so it uses a default of 0.105 nm. For MARTINI, one water bead represents four water molecules. That difference in representation is why the default distance can lead to solvent beads being placed too close and can produce clashes or an unsuitable solvent density.
The practical fix: when you add solvent, open the solvent options and increase the default van der Waals distance. The tutorial gives 0.21 nm as an example. Treat that as a starting point from the documented workflow, not a universal value for every coarse-grained force field or system.
A preparation sequence that avoids common oversights
Start with a valid coarse-grained model and keep its structure and topology files together. If you generated the model with Martinize2, select the output folder containing files such as *_CG.pdb and *_CG.top. In GROMACS Wizard, choose Prepare, set the input source to Folder, browse to that folder, and check that the expected PDB, TOP, and ITP files are detected.
Load the detected PDB file. This step loads the system into a document and computes its periodic box. If the model was generated with Martinize2 for MARTINI v.3.0.0, check that the force field is set to martini_v.3.0.0 and that the solvent model is the default Martini water. If your model uses another coarse-grained force field, you need to provide that force field rather than assume the MARTINI setting applies.
Next, enable Add solvent and open its options. Increase the default van der Waals distance—for example, to 0.21 nm—before preparing the system. Other solvent options can remain at their defaults according to the tutorial. A custom coarse-grained solvent model is also possible, but it must be provided as part of the setup.
Box and ions: two details worth checking
Review the periodic box before preparation. You can adjust the solute-to-box distance; the tutorial recommends at least 1 nm to ensure the minimum distance between periodic images. You can also choose a rhombic dodecahedron, described in the documentation as the smallest and most regular space-filling unit cell.
If you want to neutralize the system or add salt, remember that ions are added by replacing solvent molecules. That means Add solvent must be enabled for ion addition. Select the positive and negative ions, then provide salt-concentration parameters if you want additional ions beyond neutralization.
Once the settings are ready, click Prepare. You can load and inspect the prepared structure before moving on. After checking it, use the Minimize tab and its auto-fill button to pass the previous preparation result into minimization. The tutorial also notes that position-restraint options can be populated based on POSRES* definitions in the topology, so it is useful to check those settings if your model includes restraints.
Quick checklist: keep topology and structure files together; confirm the intended force field; increase the solvent van der Waals distance for the coarse-grained setup; review the box; and enable solvent if you need ions. These small checks help prevent preparation settings from being mistaken for a problem with the model itself.
For the full walkthrough and screenshots, see the GROMACS Wizard tutorial for coarse-grained systems.
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