If you’ve ever felt limited by default index groups when running GROMACS simulations, you’re not alone. Often, researchers require more flexibility to isolate and analyze specific parts of a system—say, alpha helices, or a specific chain of interest. Manually creating these custom index groups using gmx make_ndx in a terminal can be tedious, especially when working with complex structures.
The GROMACS Wizard Extension in SAMSON simplifies this process, allowing you to interactively define and manage custom index groups through a graphical interface. No command line needed. Here’s how it can help you work faster and smarter 👇
Why Bother with Custom Index Groups?
When analyzing molecular dynamics simulations, you’ll often want to track the behavior of particular residues, monitor distances between functional domains, or apply pulling forces to specific atoms. GROMACS will generate standard index groups like Protein, Water, and Ion, but more nuanced groups need to be defined manually.
How SAMSON Makes It Easier
Within SAMSON, once you’ve selected your molecular system in the GROMACS Wizard interface, look for the button labeled Add/edit index groups. This opens a window in which you can use SAMSON’s powerful selection tools to define a new group visually—no syntax required.
Let’s say you want a group for all residues forming alpha helices. Navigate to Select > Residues > Amino acids > Secondary structure > Alpha helices. Once selected, click on Generate based on current selection in document.
The GROMACS Wizard will generate a selection string compatible with gmx make_ndx automatically. You can name your new group—for example, HELICES—and add it to the index list.
Where These Groups Live
The custom groups are saved in an index.ndx file in your project directory and are fully integrated into subsequent GROMACS steps—minimization, equilibration, and production runs. You can also revisit and modify your custom groups at any point later during setup.
Note: To create custom index groups, SAMSON expects your system to have unique and consecutive indices for atoms and residues. Make sure your model is clean and properly preprocessed.
Useful, Especially for Advanced Workflows
For workflows like umbrella sampling or pulling simulations, defining groups such as specific domains, ligand-binding pockets, or individual chains becomes necessary. With SAMSON, you tap into rich molecular selection tools that let you visually pick structures, generate exact strings, and avoid mistakes common in manual input.
To learn more, visit the full documentation page on preparation steps in the GROMACS Wizard: https://documentation.samson-connect.net/tutorials/gromacs-wizard/preparation/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.