A coarse-grained model can look ready for simulation and still run into trouble during preparation. One easily missed detail is the distance used when adding solvent. In a MARTINI model, a water bead represents four water molecules, so a default van der Waals distance that works for an atomistic system may place coarse-grained solvent beads too close to the solute.
This guide focuses on a practical preparation workflow in SAMSON’s GROMACS Wizard: load the model and topology together, build the periodic box, set a suitable solvent distance, and add ions only when solvent replacement is possible. It is aimed at modelers who already have a coarse-grained model and want to avoid common setup oversights before minimization and molecular dynamics.
Start with a complete input folder
In GROMACS Wizard, open the Prepare tab and set the system source to Folder. Select the folder containing the model’s structure and topology files. For a model generated with Martinize2, use the output folder containing files such as *_CG.pdb and *_CG.top, along with the associated topology files. Keeping these files together helps the wizard detect the inputs it needs.
Once the folder is selected, check the detected PDB, TOP, and ITP files. Load the PDB using the adjacent Load button: this loads the structure into a document and computes a periodic box for it.
Check the force field before preparation
For a coarse-grained system prepared with Martinize2 for MARTINI 3.0.0, verify that the force field is set to martini_v.3.0.0. The wizard may switch to it automatically and select its default Martini water model, but checking this setting is worthwhile. If your model uses a different coarse-grained force field, provide the appropriate custom force field rather than assuming the MARTINI setting applies.
Why the solvent distance matters
If you want to solvate the system, enable Add solvent and open its options. Increase the default van der Waals distance to, for example, 0.21 nm. 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: each Martini water bead represents four water molecules.
The practical takeaway is simple: do not leave this particular default unquestioned when preparing a coarse-grained system for solvation. Adjust the distance in the solvent options, while leaving the other options at their defaults unless your system requires otherwise. A custom coarse-grained solvent model is also possible.
Box size and ions: two related checks
Review the periodic box before running preparation. If needed, change its size or unit cell type. The solute-box distance should be at least 1 nm to ensure the minimum distance between periodic images. A rhombic dodecahedron is another available unit-cell choice; it is described in the tutorial as the smallest and most regular space-filling unit cell.
You can also choose positive and negative ions to neutralize the system, or specify additional ions using a salt concentration. There is an important dependency: ions are added by replacing solvent molecules. Therefore, enable Add solvent if you want to neutralize the system or add ions. Without solvent, there are no solvent molecules for that replacement step.
Prepare, inspect, then continue
After checking the input files, force field, solvent distance, box, and ion settings, click Prepare. You can load the resulting structure to inspect it or proceed to minimization. The prepared document also contains index groups created by GROMACS; double-clicking a group selects its associated structure. SAMSON can detect coarse-grained systems for visualization as connected beads, and it colorizes water blue and ion beads according to the CPK colors of their corresponding atoms.
Before moving on, remember the key checks: keep the structure and topology files together, confirm the intended force field, increase the coarse-grained solvent van der Waals distance when solvating, and enable solvent if adding ions. Continue with energy minimization after preparation, then follow the equilibration and production steps as appropriate.
For the complete walkthrough, see the GROMACS Wizard guide to coarse-grained systems.
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