One of the challenges molecular modelers often face when working with coarse-grained (CG) molecular dynamics simulations is properly setting up force fields—particularly for MARTINI-based systems. A mismatch in force field parameters can lead to hours of debugging, poor system stability, or meaningless results 💥. This blog post guides you through how the GROMACS Wizard in SAMSON simplifies the process of assigning the MARTINI v.3.0.0 force field during CG system preparation, helping you set things up correctly and efficiently.
What Makes CG Force Field Setup Tricky?
Unlike all-atom simulations, CG models use beads to represent groups of atoms, and their accuracy relies heavily on using consistent force field parameters. When these parameters aren’t properly configured—often due to mismatched files or incorrect solvent models—your simulations may fail or give unexpected outcomes. This is especially true for MARTINI models, which come with specific considerations like bead sizes, solvent densities, and ion parameters.
How GROMACS Wizard Handles MARTINI v.3.0.0 Automatically
When preparing a MARTINI-based CG model in SAMSON using GROMACS Wizard, you can start by selecting a folder generated by Martinize2, the SAMSON Extension used to build CG models.
After choosing your structure and topology files (.pdb and .top), GROMACS Wizard smartly detects the MARTINI CG setup and automatically switches the force field to martini_v.3.0.0.
This means less room for error and a faster path to simulation.
This built-in MARTINI v.3.0.0 force field is optimized for coarse-grained simulations and includes the necessary solvent model (e.g., Martini water) and other associated parameters. If your system was built in Martinize2, this automation ensures a consistent parameter set across your workflow.
What If You’re Using a Different Force Field?
If your CG system wasn’t built with Martinize2, the Wizard allows you to provide your own custom force field and solvent model. This keeps it flexible for modelers using alternative CG representations or custom parameter sets.
See the guide on using custom force fields to learn how to integrate other models into the process.
A Tip on Solvent Setup 🧪
Before running your simulation, make sure to adjust the default van der Waals distance when solvating the system. Why? CG beads like Martini water represent groups of molecules (e.g., 4 water molecules per bead), and the default vdw distance used by GROMACS (0.105 nm) is too small. To avoid clashes and get correct solvent densities, increase the vdw distance to about 0.21 nm.
Summary
Correctly configuring your CG model’s force field saves you from unstable simulations and gets you running meaningful molecular dynamics faster. Using the GROMACS Wizard in SAMSON—especially in combination with Martinize2—makes it easy to assign the right MARTINI v.3.0.0 force field out of the box. This ensures a consistent, validated setup that eliminates one of the most common sources of simulation error in coarse-grained modeling workflows.
To learn more, read the original documentation page: GROMACS Wizard – Coarse-grained systems.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.