Preparing a coarse-grained (CG) model for molecular dynamics can look straightforward: load the structure, add water, add ions, and move on to minimization. But solvent placement has a detail that is easy to miss. A default van der Waals distance that is reasonable for an atomistic system may be too small for coarse-grained beads. The result can be an awkward starting structure, just when you want a clean system to simulate.
This workflow shows how to prepare a CG model in GROMACS Wizard, with particular attention to the solvent setting that helps avoid placing solvent beads too close to the solute. The example uses a MARTINI v.3.0.0 model generated with Martinize2.
Start with the complete model files
Keep the CG structure and its topology files together in one folder. In GROMACS Wizard, open the Prepare tab, set the system source to Folder, and choose that folder. For a Martinize2 output, look for files such as *_CG.pdb and *_CG.top, along with the related topology files.
Once the files are detected, load the PDB. This creates a document and computes a periodic box for the system. If the model came from Martinize2, check that the force field is set to martini_v.3.0.0 and that the default Martini water model is selected. If you are using a different CG force field, it needs to be supplied rather than assuming the MARTINI settings apply.
Why coarse-grained solvent needs a check
When adding solvent, open the solvent options and review the default van der Waals distance. GROMACS does not have van der Waals distances defined for CG models in this situation, so the default value may be used. The tutorial gives 0.105 nm as that default and suggests increasing it—for example, to 0.21 nm.
The reason is the scale of the model: a MARTINI water bead represents four water molecules. A distance that seems small in an atomistic context can therefore put CG solvent beads too close to other beads. Increasing this setting helps avoid clashes and supports appropriate solvent density. The documented 0.21 nm value is an example to start from; the key practical lesson is to check the setting instead of accepting the atomistic default without review. Other solvent options can remain at their defaults according to the tutorial.
Box, solvent, and ions: the order matters
Review the periodic box before preparation. The solute-to-box distance should be at least 1 nm to maintain the minimum distance between periodic images. You can also choose a rhombic dodecahedron, a compact, regular space-filling unit cell.
If the system needs neutralization or added salt, enable solvent as well. Ions are added by replacing solvent molecules, so the ion options depend on solvent being present. Select the positive and negative ions, then choose additional salt settings if needed. This dependency is worth remembering when an ion option does not seem to fit the setup: solvent is part of the preparation, not an unrelated later step.
When the settings are ready, click Prepare. You can load and inspect the resulting structure, or continue to minimization. A useful final check is to confirm that the prepared system contains the expected solvent and ions and that the periodic box has the intended dimensions.
Continue with minimization and equilibration
After preparation, switch to the Minimize tab and use the auto-fill button to take the previous step’s output as the input structure. In the advanced parameters, position restraints are populated based on the POSRES* definitions in the topology files. If restraints were generated by Martinize2, their names can correspond to individual molecules, so check which restraint applies before using it for minimization or equilibration.
The larger takeaway is simple: CG preparation is not just atomistic preparation with fewer particles. Confirm the force field, review the solvent distance, and remember that ions replace solvent. Those checks help catch avoidable setup problems before spending time on simulation.
For the complete walkthrough, see the GROMACS Wizard coarse-grained systems tutorial.
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