If you use GROMACS for molecular dynamics simulations, you’ve likely encountered the concept of index groups. While GROMACS automatically generates standard groups (like Protein, Solvent, etc.), custom index groups are essential when you need fine control during analysis or for defining special simulation parameters.
For example, umbrella sampling or calculating distances between specific atoms becomes much easier if the relevant groups are properly defined from the beginning. But creating these custom index groups manually with gmx make_ndx can be tedious — especially for users working with complex systems or large sets of conformations.
This is where SAMSON’s GROMACS Wizard offers a helpful solution that simplifies this process with a graphical interface tightly integrated with selection tools.
Why Custom Index Groups?
- Define specific atoms or regions for pulling, restraints, or analysis.
- Simplify the setup of advanced simulations like umbrella sampling.
- Group functionally relevant motifs across multiple simulation steps.
And critically: your indexing only needs to be defined once, and can be reused in minimization, equilibration, and full simulation stages.
How It Works in SAMSON
Once your system is set in the GROMACS Wizard, you can click on Add/edit index groups.
A separate window pops up, allowing you to add new index groups through two easy ways:
- Use GROMACS syntax manually.
- Use the visual selection tools from SAMSON and auto-generate the GROMACS selection string.
Let’s take an example. If you want to define an index group for residues in alpha helices, you can do this entirely visually:
- In the main SAMSON viewport, select Select > Residues > Amino acids > Secondary structure > Alpha helices.
- Click Generate based on current selection in document.
- Name the group (e.g.,
HELICES) and click Add index group to the list.
That’s it — the index group will be saved and passed to GROMACS using gmx make_ndx, and stored in the index.ndx file inside your project folder.
Some Notes to Keep in Mind
- Your system must use unique and consecutive indices for atoms and residues for this feature to work correctly.
- These custom groups are available right away and persist through the different stages of your workflow.
- You can create or edit index groups again during minimization, equilibration, or simulation if needed.
This feature significantly reduces the time spent jumping between tools to organize your simulation. For researchers running complex batch simulations or modeling dynamic pathways, predefining the right groups can be game-changing for efficiency and clarity later in the workflow.
To explore this topic further, visit the official documentation page on adding custom index groups.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.