The small distance setting that can make coarse-grained solvation go wrong

Preparing a coarse-grained (CG) model for molecular dynamics can look straightforward: load the structure, add water, and continue to minimization. But a setting that is reasonable for an atomistic system may be too small for a coarse-grained one. The result can be solvent beads placed too close to the solute, creating clashes or an unsuitable starting arrangement.

This matters especially for MARTINI models. A Martini water bead represents four water molecules, so it is not the same size as a single atomistic water molecule. The GROMACS Wizard tutorial highlights a specific source of trouble: GROMACS does not have van der Waals distances defined for CG models in this case, so it uses a default distance of 0.105 nm. That can be too close for CG beads.

The practical adjustment is simple: when adding solvent, open the solvent options and increase the default van der Waals distance. The tutorial gives 0.21 nm as an example. Treat this as a starting value from the documented workflow, rather than a universal setting for every CG force field or system.

A preparation sequence that avoids common snags

1. Start with a complete model. Keep the CG structure and topology files together in one folder. For a Martinize2-generated model, select the output folder containing files such as *_CG.pdb and *_CG.top, along with the related topology files.
2. Load the structure to compute the box. In GROMACS Wizard’s Prepare tab, choose Folder as the input source, select the model folder, and load the detected PDB file. Loading it computes a periodic box for the system.
3. Confirm the force field. For a model generated with Martinize2 for MARTINI v.3.0.0, check that the force field is set to martini_v.3.0.0 and that the expected Martini water model is selected. If the model uses another CG force field, provide the appropriate custom force field instead of assuming the automatic MARTINI selection applies.
4. Set the solvent distance before solvation. Enable Add solvent, open its options, and increase the van der Waals distance—for example, to 0.21 nm as described in the tutorial. Other solvent options can remain at their defaults for this example.
5. Check the periodic box and ion settings. If needed, adjust the box dimensions. 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. To neutralize the system or add salt, also enable solvent: ions are added by replacing solvent molecules.
6. Prepare, then inspect. Click Prepare. You can load the result to inspect it before moving on, or use it as the input for minimization. GROMACS Wizard can display detected CG systems as connected beads, with water shown in blue and ion beads colored according to their corresponding atoms.

The main takeaway is to treat solvation as a model-specific preparation step, not just a checkbox. For Martini CG systems, review the solvent distance because the default value may not suit the larger beads. Then confirm the force field, box, and ion choices before running preparation. These checks help catch avoidable setup problems before spending time on minimization and later simulation stages.

For the complete workflow and additional notes, see the GROMACS Wizard tutorial for coarse-grained systems.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.