Anyone who has worked with GROMACS has likely run into this issue: you want to analyze a specific part of your system—maybe all alpha helices, or a binding pocket—but the default index groups just don’t cut it. Manually configuring these groups after a simulation takes time and disrupts the workflow.
In SAMSON, you can streamline this right from the preparation step using the GROMACS Wizard. It allows you to define custom index groups before running your simulations, ensuring your analysis is easier and faster later on.
Why custom index groups matter
GROMACS automatically generates standard index groups based on your system’s structure (like Protein, SOL, or NA+). But for advanced workflows—such as pulling a specific secondary structure during steered MD, or isolating certain residues for analysis—you’ll need custom groups. Without them, you may have to reprocess trajectory files post-simulation using GROMACS command-line tools, which can be tedious and error-prone.
Create index groups visually in SAMSON
In SAMSON, you can visually select parts of your molecular system and the GROMACS Wizard will auto-generate the correct selection string for the index file. No need to memorize syntax like r 45-56 & a CA. It’s as simple as selecting your residues using a menu.
Here’s how it works:
- Click on Add/edit index groups in the GROMACS Wizard.
- Select atoms or residues in the document view, for example, using Select > Residues > Amino acids > Secondary structure > Alpha helices.
- Click Generate based on current selection in document.
- Name your group (like
HELICES) and click Add index group to the list.
This will create an entry in the index.ndx file as part of your project folder. The group is then immediately usable for future minimization, equilibration, or production MD steps.
Reusability and testing
An added benefit: you can test a selection string directly in the interface. If you’re unsure whether your selection includes the desired atoms, SAMSON highlights those atoms in the viewport immediately.
This speeds up iteration and ensures you don’t find out after a multi-nanosecond simulation that you forgot to include a key residue or that your selection syntax was off.
When should you define custom index groups?
- You’re planning umbrella sampling or steered MD, and need specific pull groups
- You want to monitor RMSD or distance between non-standard groups
- You want to extract energy contributions from user-defined regions
Why do this during preparation?
Setting index groups early integrates them naturally into your workflow—and avoids redundant trajectory parsing and make_ndx usage later. Plus, SAMSON ensures the indices are consistent and saved as part of your project.
To summarize, setting up custom index groups during preparation in SAMSON is a small step that yields big benefits in clarity, reproducibility, and time saved when analyzing your simulations.
Learn more in the GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.