When running molecular dynamics simulations with GROMACS, index groups are often an overlooked but essential part of analyzing results and defining simulation subsets. Whether you’re calculating RMSD, defining pulling groups, or setting restraints, the flexibility to define your own index groups can be incredibly useful.
Fortunately, the GROMACS Wizard in the SAMSON platform makes creating custom index groups straightforward—even for those without deep command-line experience. In this post, we’ll explore what custom index groups are, why they matter, and how to define them inside the SAMSON interface efficiently.
What Are Index Groups in GROMACS?
Index groups in GROMACS are subsets of atoms or residues defined by users or automatically generated by GROMACS commands such as gmx make_ndx. These groups are saved in the index.ndx file, which is essential for many GROMACS tasks—ranging from analysis (RMSD, RDFs, etc.) to simulation input definitions (like position restraints or umbrella pulling).
Why Define Custom Index Groups?
Standard groups in GROMACS usually include whole molecules, proteins, water, and ions. However, for more complex tasks—like pulling on specific secondary structures, calculating localized RMSD, or focusing on a few residues of interest—you’ll need your own groups.
Custom index groups let you go beyond defaults and tailor simulation and analysis to your specific needs. If you’re performing analyses based on secondary structure elements (alpha helices, β-sheets), or if certain residues are critical in your experimental system, defining them as groups can save time and improve results.
How to Create Custom Index Groups in SAMSON
In the GROMACS Wizard Prepare step, once your system is set, you’ll see the button Add/edit index groups. Clicking this opens a simple dialog where you can define your custom groups.
Here’s how it works:
- Use SAMSON’s visual interface to select atoms or residues. For example: Select > Residues > Amino acids > Secondary structure > Alpha helices.
- Once selected, click Generate based on current selection in document.
- Name your group (e.g.,
HELICES), and click Add index group to the list.
This automatically prepares the correct selection string using GROMACS syntax, meaning no need to remember atom numbers manually.
Once added, your group appears in the list and is stored in the index.ndx file. These groups will be accessible for later stages (minimization, equilibration, simulation), and for post-run analysis.
Requirements and Notes
- Residue and atom indices must be unique and consecutive for the feature to work correctly.
- This step is optional, so you can proceed without it—but if your simulation has specific analysis needs, it’s worth doing.
- You can also define or edit index groups later in your workflow.
Adding groups in a graphical interface eliminates the trial-and-error that often comes with using make_ndx via the terminal. The selection mechanisms in SAMSON are powerful and intuitive, helping modelers save time and reduce errors.
To learn more about the entire preparation workflow and other powerful features in the GROMACS Wizard, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.