A coarse-grained system can look ready for simulation and still run into trouble at the preparation stage. One easy-to-miss detail is solvent placement: the default van der Waals distance used by GROMACS may be too small for coarse-grained beads. The result can be an unsuitable solvent arrangement around the model.
This walkthrough focuses on preparing a coarse-grained system in GROMACS Wizard, with particular attention to the solvent setting that matters for MARTINI models. It also covers the surrounding steps—loading the right files, defining the box, and adding ions—so that the key setting has a clear place in the workflow.
Start with the complete model folder
Before opening the preparation workflow, make sure you have a valid coarse-grained model. If it was generated with Martinize2, keep the structure and topology files together in the same folder. In GROMACS Wizard, open the Prepare tab and set the system source to Folder. Browse to the folder containing the model files, such as the generated *_CG.pdb and *_CG.top.
After selecting the folder, check that GROMACS Wizard detects the PDB, TOP, and ITP files. Load the detected PDB file: this loads the system into a new document and computes a periodic box.
For a Martinize2 model made with MARTINI v.3.0.0, confirm that the force field is set to martini_v.3.0.0. The software switches to this force field automatically for such a system, but it is still worth verifying. If your model uses another coarse-grained force field, you need to provide that force field rather than assume the MARTINI setting applies.
Why the solvent distance needs attention
If you want to solvate the model, enable Add solvent and open its options using the gear button. Increase the default van der Waals distance to, for example, 0.21 nm.
The reason is specific to coarse-grained models: GROMACS does not have van der Waals distances defined for these models, so it uses the default value of 0.105 nm. That can be too close for coarse-grained beads. In MARTINI, each water bead represents four water molecules, so using the larger example distance helps avoid clashes and supports proper solvent density. Other solvent options can remain at their defaults.
This is a useful setting to check before running preparation: it is easy to overlook because the default is already filled in, and the reason to change it is tied to the coarse-grained representation rather than an obvious visual warning.
Set the box, then add ions
Review the periodic box size. If needed, increase the solute-box distance; the documentation recommends at least 1 nm to ensure the minimum distance between periodic images. You can also choose a Rhombic dodecahedron, a compact, regular space-filling unit cell.
To neutralize the system or add ions at a chosen salt concentration, select the positive and negative ions and provide the relevant parameters. One dependency matters: ions are added by replacing solvent molecules, so the Add solvent option must be enabled when adding ions.
When the settings are ready, click Prepare. You can then load and inspect the prepared structure, or continue to minimization. The resulting document includes GROMACS index groups, which you can double-click to select their associated structures. SAMSON also attempts to detect coarse-grained systems for visualization, displaying them as connected beads and coloring water blue.
Carry the prepared system into simulation
After checking the prepared structure, move to the Minimize tab and use the auto-fill button to set the previous step’s results as the input. Advanced preprocessing options include position restraints, which are filled based on the POSRES* defines in the topology files. If Martinize2 generated restraints for the backbone or all particles, its topology files can contain separate restraint records for each molecule; if restraints were disabled, there will be none.
The practical takeaway: for coarse-grained preparation, verify the input files and force field, deliberately adjust the solvent van der Waals distance, and remember that adding ions requires solvent. These checks help address common setup issues before moving on to minimization and equilibration.
For the full workflow and related steps, see the GROMACS Wizard coarse-grained systems tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.