When preparing coarse-grained (CG) molecular dynamics simulations with the MARTINI force field, many modelers spend time double-checking whether they’ve configured the correct parameters and files. One small but frequent pitfall is using a CG topology—often from Martinize2—but forgetting to assign the right force field in GROMACS before simulation.
This blog post shows how the GROMACS Wizard Extension for SAMSON helps you avoid this mistake entirely—with a built-in automatic switch to the martini_v.3.0.0 force field as soon as your CG topology is loaded.
What’s the issue?
When using CG systems like those generated via Martinize2, structures and topologies are usually exported as .pdb and .top files that follow the MARTINI format. But if the wrong force field is selected later in GROMACS, this can lead to incompatible parameters, errors during preprocessing, or incorrect simulation outcomes. The problem is especially easy to miss if you’re deeply focused on other setup tasks.
How the GROMACS Wizard does it better
When importing your CG model into the GROMACS Wizard (via the Prepare tab), the wizard examines the input structure and topology files. If it detects they follow the MARTINI CG conventions—as is the case when your files include names like *_CG.pdb and *_CG.top—it automatically switches the force field to martini_v.3.0.0.
This force field is shipped directly with the GROMACS Wizard extension, so you don’t need to install or download anything extra for it to work.
But what if I’m using a custom CG force field?
Here, the wizard is smart in a different way: if no known CG topology is detected, or if you’re using a modified version, the wizard allows you to manually define and provide a custom force field. In that case, refer to the custom force field section in the documentation to ensure proper setup.
Check before moving on
After loading your CG model, double-check that the force field section of the UI shows martini_v.3.0.0. This simple step makes all further stages—including solvation, ion addition, and MD protocols—much smoother.
Miscommunication between topology formats and force field expectations can cost hours if you face errors later during minimization or equilibration. The GROMACS Wizard reduces this friction by helping you make the right assumptions earlier on.
📘 Learn more in the full tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.