Preparing a coarse-grained model for molecular dynamics can involve a surprisingly easy-to-miss detail: the distance used when adding solvent. A value that works for an atomistic system may be too small for coarse-grained beads. The result can be an awkward starting configuration, just when you want to move on to minimization and equilibration.
This guide focuses on a practical preparation workflow in GROMACS Wizard, with particular attention to solvent settings for a MARTINI v.3.0.0 system. The key lesson is simple: check the force field, and review the van der Waals distance before solvating.
Start with a complete input folder
GROMACS Wizard can prepare a coarse-grained model from a folder containing its structure and topology files. In the Prepare tab, set the system source to Folder, browse to the folder, and check that the expected files are detected. For a model produced with Martinize2, use its output folder, which should contain files such as *_CG.pdb and *_CG.top, along with related topology files.
Load the detected PDB file. This loads the model into a document and computes a periodic box, providing the starting point for preparation.
Confirm the force field before adding solvent
For a system generated with Martinize2 for MARTINI v.3.0.0, GROMACS Wizard should switch to the included martini_v.3.0.0 force field and set the default Martini water model. Confirm that the force field selection is correct rather than assuming it was detected as intended. If your model uses a different coarse-grained force field, provide that force field using the custom-force-field workflow.
This check matters because the force field and solvent model need to match the model you are preparing. A MARTINI example is not a universal setting for every coarse-grained system.
Review the van der Waals distance
If you want to solvate the system, enable Add solvent and open its options. For coarse-grained models, increase the default van der Waals distance to, for example, 0.21 nm.
Why change it? GROMACS does not have van der Waals distances defined for coarse-grained models in this situation, so it uses a default value of 0.105 nm. That distance may be too small for coarse-grained beads. In the MARTINI water model, each water bead represents four water molecules, so using the larger example value helps avoid clashes and supports appropriate solvent density. Other solvent options can remain at their defaults unless your setup requires a custom solvent model.
Box size and ions: two connected choices
Check the periodic box as part of preparation. If you adjust the solute-to-box distance, the tutorial notes that it should be at least 1 nm to ensure the minimum distance between periodic images. A rhombic dodecahedron is another available unit-cell choice.
You can also choose ions to neutralize the system or add additional salt. The important dependency is that ions are added by replacing solvent molecules: to neutralize the system or add ions, you must enable solvent addition. Set the desired ion and salt options, then click Prepare.
Check the prepared system before continuing
After preparation, load and inspect the structure if needed, or proceed to minimization. In the document, GROMACS-created index groups can be opened to select their associated structures. For minimization, switch to the Minimize tab and use the auto-fill button to take the previous step’s results as the input structure.
A useful preflight checklist is: the structure and topology files are together; the expected force field is selected; the coarse-grained solvent distance has been reviewed; the box is suitable; and solvent is enabled if you plan to add ions. Checking these items before running preparation can help prevent avoidable setup problems.
For the complete walkthrough and related steps, see the GROMACS Wizard tutorial for coarse-grained systems.
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