A coarse-grained system can look ready for simulation and still run into trouble at the solvation stage. One easy-to-miss detail is the van der Waals distance used when adding solvent. A value that may be suitable as a general default can be too small for coarse-grained beads, leaving solvent packed too close to the model.
This matters especially for MARTINI: a water bead represents four water molecules, rather than one atom-sized water molecule. GROMACS Wizard may use a default van der Waals distance of 0.105 nm when distances for the coarse-grained model are not defined. The tutorial recommends increasing this setting—for example, to 0.21 nm—to help avoid clashes and achieve appropriate solvent density.
A practical preparation sequence
Start with a valid coarse-grained structure and its topology. If the model was generated with Martinize2, keep the generated files together in one folder. In GROMACS Wizard, open the Prepare tab, set the system source to Folder, and select the folder containing the structure and topology files. For a Martinize2 model, look for files such as *_CG.pdb and *_CG.top.
After the files are detected, load the PDB. This lets GROMACS Wizard compute a periodic box for the system. If the model uses 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 expected Martini water. Models using another coarse-grained force field require the corresponding force field to be provided.
Adjust the solvent distance
To solvate the system, enable Add solvent and open its options. Increase the default van der Waals distance; the tutorial gives 0.21 nm as an example. The reason is not simply that the system is larger: coarse-grained beads represent groups of atoms, so applying a short default distance can place solvent beads unusually close to the solute.
The value shown is a useful starting point from this workflow, not a universal setting for every coarse-grained model. The page advises leaving the other solvent options at their defaults unless you have a reason to change them. You can also use a custom coarse-grained solvent model when your setup calls for one.
Keep the box and ions in mind
Solvent spacing and periodic-box size are separate settings. If you need to adjust the box, the tutorial notes that the solute-to-box distance should be at least 1 nm to maintain the minimum distance between periodic images. You may also choose a rhombic dodecahedron, a compact, regular space-filling unit cell.
To neutralize the system or add salt, enable solvent first: ions are added by replacing solvent molecules. Choose the positive and negative ions, then configure any additional salt concentration you want to include. Once the preparation settings are ready, click Prepare. You can load and inspect the resulting structure before moving on.
After preparation
Check that the prepared system looks as expected, then continue to minimization. In the Minimize tab, the auto-fill button sets the previous preparation result as the input structure. Advanced parameters also show position-restraint options detected from topology definitions; for Martinize2 models, restraint records can be generated separately for each molecule.
The useful habit is to treat coarse-grained solvation as a model-specific step: confirm the force field, deliberately review the solvent distance, and remember that ions require solvent to be present. For the complete workflow and screenshots, see the GROMACS Wizard guide to coarse-grained systems.
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