Setting up molecular simulations in GROMACS often involves intricate configuration. One commonly overlooked step that can save time and add flexibility is defining custom index groups. If you’ve ever scrolled through a sea of atoms and residues to define simulation regions, analysis sets, or umbrella sampling groups, this feature will simplify your workflow.
In GROMACS, index groups are collections of atoms used in many simulation steps, such as position restraints or pull code. By default, GROMACS defines groups like Protein, Water, or Ion, but for detailed analyses, you might need more specific groups.
Fortunately, with the GROMACS Wizard in SAMSON, creating and managing these groups is visual, intuitive, and integrated into the preparation workflow.
Adding Index Groups Visually
SAMSON leverages its selection interface to help you define groups directly from the structure. You can:
- Use visual selection tools (like by residue, atom name, or secondary structure).
- Automatically generate GROMACS-compatible selection strings.
- Preview and test your groups before saving them.
Let’s walk through an example: defining a group of residues in alpha helices.
First, select the residues via Select > Residues > Amino acids > Secondary structure > Alpha helices.
Then, click the Add/edit index groups button to open the index group editor.
In the editor, generate the selection string based on your current selection with one click:
Name your group (e.g., HELICES) and add it to the project:
The group appears in the index group list and will be saved in the index.ndx file generated by GROMACS at preparation time.
Why This Matters
Researchers using GROMACS often prepare dozens of systems, each requiring individualized restraints or analysis windows. With SAMSON’s GROMACS Wizard, defining reusable groups early on makes future steps more structured and reproducible.
For example, during umbrella sampling, having pre-defined pull groups in the index file avoids manually hunting atom indexes each time you run gmx make_ndx. Moreover, your groups remain linked to your project in SAMSON, streamlining visualization and validation.
And if you’re working with coarse-grained or multi-chain systems, grouping atoms correctly from the start ensures compatibility across various setups.
When and Where to Use It
Adding custom index groups is optional, but beneficial in scenarios where:
- You need precise control during simulations (e.g., position restraining parts of a system).
- You plan advanced sampling techniques like umbrella sampling.
- Analysis requires grouping atoms by biochemical function or structure.
Tip: Custom groups can also be added later during the minimization, equilibration, or production stages—but adding them early increases reproducibility and clarity.
To learn more about adding custom index groups and preparing systems with the GROMACS Wizard, visit the official documentation page: GROMACS Wizard Preparation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.