Molecular modelers working with coarse-grained (CG) force fields know that preparing a CG system in GROMACS can be a tricky and time-consuming process. The need to manually process topology files, create solvent environments, define boxes, and manage ions can become overwhelming—especially when small errors cause significant delays or failed simulations.
Fortunately, the GROMACS Wizard Extension in SAMSON simplifies this process with a visual, step-by-step experience tailored for CG modeling. In this post, we’ll walk through preparing a coarse-grained system of a soluble protein using the extension, with guidance and smart defaults specific to the MARTINI v.3.0.0 force field.
Start With the Martinize2 Output
If your system has already been coarse-grained using the Martinize2 SAMSON Extension, simply point GROMACS Wizard to the folder containing the generated *.pdb and *.top files.
Load and Visualize the System
Once the folder is selected, detected input files (PDB, TOP, ITP) will be listed. Click the Load button next to the PDB file to view and compute a periodic box for the system. SAMSON provides an interactive 3D view, making it easy to inspect structures and settings.
Select Force Field and Solvent Model
The wizard automatically switches the force field to martini_v.3.0.0 and sets the solvent model to Martini water when it detects a Martinize2 CG structure. Verifying that settings match your model is just a click away.
Solvate with Correct Parameters
When adding solvent, increase the van der Waals distance to approximately 0.21 nm. This is essential: GROMACS uses a default value suited for atomistic models, which can be too small for CG systems and lead to overlapping beads or poor solvent packing.
Define the Box and Add Ions
Customize box dimensions and shape. A Rhombic dodecahedron box is often more efficient. You can then neutralize the system by selecting ion types and defining a salt concentration. The wizard automatically adds ions by replacing solvent molecules, ensuring physical relevance and consistency.
Click Prepare
Finally, after verifying all parameters, click the Prepare button. Within seconds, you’ll receive a fully ready CG system that can be visualized and exported for minimization and MD simulation steps.
Why This Matters
Setting up CG systems in GROMACS used to involve careful manual edits and required expert-level knowledge of force fields and file formatting. Now, with this extension in SAMSON, the entire process is visual, consistent, and reproducible. Once your prepare step is complete, you can immediately continue to minimization or equilibration workflows with confidence.
For full instructions, including how to use custom force fields or solvents, visit the complete tutorial at SAMSON Documentation: GROMACS Wizard – Coarse-Grained Systems.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.