A coarse-grained system can look ready for simulation and still run into trouble during preparation. One easily missed cause is the distance used when adding solvent. In a MARTINI model, a water bead represents several water molecules, so a default distance intended for other systems may place solvent beads too close to the coarse-grained particles.
This is a practical issue for molecular modelers preparing a CG structure for molecular dynamics: the structure and topology may be present, and the system may load correctly, but solvent placement still needs attention. Here’s a preparation workflow that helps avoid that avoidable mismatch.
Start with a complete input folder
GROMACS Wizard can prepare a CG model from a folder containing the structure and topology files. For the example workflow, that means selecting the folder containing the model’s .pdb and .top files, along with any related topology files such as .itp. If you generated the model with Martinize2, use its output folder so the generated files stay together.
In GROMACS Wizard, open the Prepare tab, set the system source to Folder, and browse to the input folder. Check that the expected PDB, TOP, and ITP files are detected. Then click Load next to the PDB file. This loads the structure into a document and computes a periodic box.
Check the force field before preparing
For a CG model generated by Martinize2 for MARTINI 3.0.0, GROMACS Wizard should switch to the shipped martini_v.3.0.0 force field and use its default Martini water model. Confirm the force field selection before continuing. If your model uses a different CG force field, you’ll need to provide that force field rather than assume the MARTINI setting is appropriate.
Give coarse-grained solvent enough room
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. The documented default is 0.105 nm; GROMACS does not have van der Waals distances defined for CG models in this case, so it uses that default. It may be too small for CG beads, since each Martini water bead represents four water molecules.
This setting matters because solvent placement is not just a checkbox: the distance influences how closely solvent beads can be placed relative to the model. For this workflow, changing the distance is the key preparation detail to check before running the setup.
You can leave the other solvent options at their defaults, or provide a custom CG solvent model if your setup requires one.
Review the box and ions
Check the periodic box size and shape. The solute-box distance should be at least 1 nm to ensure a minimum distance between periodic images. A rhombic dodecahedron is another available unit-cell choice and is described in the tutorial as a small, regular space-filling cell.
If you need to neutralize the system or add salt, select the positive and negative ions and set any additional salt-concentration parameters. Remember that ions are added by replacing solvent molecules, so the Add solvent option must be enabled when adding ions.
Prepare, inspect, then continue
Click Prepare. You can load and inspect the prepared structure before moving on, or continue to minimization. SAMSON can display detected CG systems as connected beads; water is colored blue, and ion beads are colored using CPK colors for their corresponding atoms.
Before leaving the preparation step, it’s worth checking four things: the folder contains the model’s structure and topology files; the force field matches the model; the solvent distance has been increased for CG solvation; and the box and ion settings reflect your intended setup. These checks address common setup mismatches without changing the model itself.
Once the prepared system is ready, continue with energy minimization, followed by equilibration and production molecular dynamics. For the full walkthrough, see the GROMACS Wizard tutorial for coarse-grained systems.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.