A coarse-grained system can look ready for simulation and still run into trouble during preparation. One easy-to-miss source of problems is solvent placement: the default van der Waals distance used when adding solvent may be too small for coarse-grained beads. The result can be water placed uncomfortably close to the model you are trying to simulate.
This matters especially for MARTINI-style models. A Martini water bead represents four water molecules, so it is not equivalent in size to a single atomistic water molecule. In GROMACS Wizard, the default van der Waals distance is 0.105 nm; for a coarse-grained system, the tutorial recommends increasing it—for example, to 0.21 nm—before adding solvent.
Start with the files that belong together
Before opening the preparation workflow, make sure you have a valid coarse-grained model and keep its structure and topology files together in one folder. For a model generated with Martinize2, select the output folder containing files such as *_CG.pdb and *_CG.top. GROMACS Wizard detects the PDB, TOP, and ITP files in that folder.
In the Prepare tab, set the system source to Folder, choose the folder, and click Load beside the detected PDB. Loading the structure lets the application compute a periodic box. If the model was made with Martinize2 for MARTINI 3.0.0, check that the force field is set to martini_v.3.0.0 and that the intended Martini water model is selected.
Adjust solvent placement before adding water
If you want to solvate the system, enable Add solvent and open its options using the gear button. Increase the default van der Waals distance to a suitable coarse-grained value, such as 0.21 nm. The purpose of this setting is to avoid placing solvent beads too close to the system and to help achieve appropriate solvent density. The tutorial explains that GROMACS does not have van der Waals distances defined for coarse-grained models in this case, so it uses the default 0.105 nm value—which may be too close for Martini beads.
You can leave the other solvent options at their defaults, or provide a custom coarse-grained solvent model if your workflow requires one. The important practical point is to review the distance rather than assuming that an atomistic default is appropriate for a bead-based model.
Check the box and plan ions together with solvent
Review the periodic box size as well. The solute-box distance should be at least 1 nm to ensure the minimum distance between periodic images. If appropriate for your system, you can also choose a rhombic dodecahedron, a compact, regular space-filling unit cell.
If you need to neutralize the system or add salt, configure the positive and negative ions and any additional salt concentration you want. There is one dependency worth remembering: ions are added by replacing solvent molecules. Therefore, enable Add solvent when adding ions.
Prepare, inspect, then continue
Once the input files, force field, solvent settings, box, and ion options are checked, click Prepare. You can load and inspect the prepared structure, including the index groups created by GROMACS, or proceed to minimization. In the Minimize tab, the auto-fill button uses the previous run’s results as the input structure. Position restraints, when present in the topology, are available in the preprocessing options; their presence depends on how the model was generated.
A useful preflight checklist: the structure and topology are together; the expected coarse-grained force field is selected; the solvent distance has been reviewed; the box has enough clearance; and solvent is enabled if ions are needed. These checks address several avoidable setup snags before you move on to minimization and equilibration.
For the complete workflow and screenshots, see the GROMACS Wizard coarse-grained systems tutorial.
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