A coarse-grained system can look ready for simulation and still run into trouble during solvation. One easily missed setting is the van der Waals distance used when placing solvent. In the GROMACS Wizard workflow described here, the default distance may be too small for Martini coarse-grained beads, potentially placing solvent too close to the solute. Understanding why—and where to adjust it—can help prevent a crowded starting structure.
Why coarse-grained solvation needs a check
In a coarse-grained model, a bead represents a group of atoms rather than a single atom. For the MARTINI model used in this tutorial, each water bead represents four water molecules. GROMACS does not have van der Waals distances defined for coarse-grained models in this context, so it uses a default distance of 0.105 nm. That value might be too close for coarse-grained beads.
The practical takeaway is simple: do not assume that the default solvent-placement distance is appropriate just because it is already filled in. Before adding solvent, open the solvent options and increase the default van der Waals distance—for example, to 0.21 nm, as suggested in the tutorial. The other solvent options can be left at their defaults.
A preparation sequence that avoids common oversights
- Start with a complete model folder. If the model was generated with Martinize2, keep the generated structure and topology files together. In GROMACS Wizard, choose Prepare, set the system source to Folder, and select the folder containing the generated files, such as the
*_CG.pdband*_CG.topfiles. - Load the structure before preparing it. Select Load next to the detected PDB file. This loads the system into a document and computes a periodic box. Check that the system and box look reasonable before continuing.
- Verify the force field. For a model generated by Martinize2 for MARTINI v.3.0.0, GROMACS Wizard should switch to
martini_v.3.0.0and use the default Martini water model. Confirm the selected force field. If you are using a different coarse-grained force field, provide the appropriate custom force field instead. - Adjust the solvent distance. Enable Add solvent, open its options, and increase the default van der Waals distance to a suitable value such as 0.21 nm. This is the key coarse-grained-specific check: the default 0.105 nm may be too small for the beads.
- Review the box and ion settings. Adjust the periodic box if needed. The tutorial recommends a solute-box distance of at least 1 nm to ensure the minimum distance between periodic images, and notes that a rhombic dodecahedron is a compact, regular space-filling unit cell. To neutralize the system or add ions, solvent must also be enabled, because ions are added by replacing solvent molecules.
Inspect before moving on
After clicking Prepare, you can load the prepared structure and inspect it before starting minimization. SAMSON can display detected coarse-grained systems as connected beads, with water colored blue and ion beads colored according to the CPK scheme. This visual check does not replace the setup choices, but it gives you a chance to review the prepared system before proceeding.
Once preparation is complete, continue to minimization and then equilibration and production molecular dynamics. In the Minimize tab, the auto-fill button can use the results of the previous step as the input structure. Position restraints, when present in the topology, can also be reviewed in the advanced preprocessing options.
The broader lesson is to treat coarse-grained solvent placement as a model-aware setting, not an automatic default. Check the force field, increase the van der Waals distance as needed, and remember that adding ions depends on having solvent enabled.
For the complete workflow and accompanying steps, see the GROMACS Wizard coarse-grained systems tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.