Preparing a coarse-grained (CG) system for molecular dynamics can seem straightforward: load the structure, add water, add ions, and move on to simulation. But there is an easy-to-miss detail in that workflow: the default van der Waals distance used during solvation may be too small for coarse-grained beads. The result can be solvent placed too close to the model.
This matters especially for MARTINI systems. A Martini water bead represents four water molecules, so its scale differs from that of atomistic water. GROMACS does not have van der Waals distances defined for CG models in this preparation context, and the default value described in the GROMACS Wizard tutorial is 0.105 nm. For CG systems, increase that distance—for example, to 0.21 nm—before adding solvent.
A practical preparation checklist
Start with a valid CG model and keep its structure and topology files together. If the model was 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 the folder; checking that the expected files are present is a useful first step before running preparation.
In the GROMACS Wizard Prepare tab, set the system source to Folder, browse to the model’s folder, and load the detected PDB. Loading it computes a periodic box for the system. If you are using the MARTINI v.3.0.0 model generated by Martinize2, verify that the force field is set to martini_v.3.0.0 and that the default Martini water model is selected. If your CG model uses a different force field, provide that force field rather than assuming the MARTINI setting applies.
Solvent and ions go together
If the system needs solvent, enable Add solvent and open its options. Increase the default van der Waals distance to a suitable CG value, such as 0.21 nm, then leave other options at their defaults unless your setup calls for a change. The tutorial also supports providing a custom CG solvent model when needed.
Planning to neutralize the system or add salt? Enable solvent as well: ions are added by replacing solvent molecules. Select the positive and negative ions for neutralization, and, if you want additional ions through a salt concentration, choose that option and provide its parameters. This dependency is easy to overlook when preparing an ion-containing system.
Check the box, then prepare
Review the periodic box before clicking Prepare. You can 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 option and is described as the smallest and most regular space-filling unit cell.
After preparation, load and inspect the structure if useful, or continue to minimization. For the next simulation step, switch to Minimize and use the auto-fill button to set the previous run’s results as the input structure. Advanced preprocessing parameters include position restraints detected from POSRES* definitions in topology files. If you generated restraints with Martinize2, check which restraint group corresponds to each molecule; if you selected no restraints there, none will be available.
The main takeaway is simple: for CG preparation, verify the force field, increase the solvent van der Waals distance, and remember that ion addition requires solvent. For the complete workflow, see the GROMACS Wizard coarse-grained systems tutorial.
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