Custom Index Groups in GROMACS Wizard: A Smart Way to Prepare for Targeted Simulations

When working with molecular systems in GROMACS, detailed analysis and advanced simulation setups such as umbrella sampling or pulling simulations often require specific selections of atoms or residues. These selections are managed using index groups. GROMACS automatically generates standard index groups—like ‘Protein’, ‘Water’, and ‘Ions’—but what if you need more?

That’s where SAMSON’s GROMACS Wizard can help.

The benefit of adding custom index groups

Being able to define your own index groups means you can:

  • Select regions of interest, such as alpha helices, active site residues, or ligands.
  • Use these groups in downstream simulation steps like pulling forces during umbrella sampling.
  • Streamline your analysis pipelines by having pre-defined atom groups that are relevant to your experiment.

And the best part? You don’t have to manually write complex GROMACS selection strings. SAMSON helps you create them visually.

How to create custom index groups in SAMSON

  1. Start by selecting the atoms or residues in your structure using SAMSON’s visual selection tools. For example, you can select all alpha helices via:

    Select > Residues > Amino acids > Secondary structure > Alpha helices

    Select alpha helices

  2. Click the Add/edit index groups button in the GROMACS Wizard.

    Add/edit index groups

  3. In the pop-up window that appears, click Generate based on current selection in document.

    Generate index group string

  4. Give your new group a name (like HELICES) and click Add index group to the list.

    Add index group

  5. Your group now appears in the list of custom groups and will be written to the index.ndx file via gmx make_ndx.

    New index group list

Why this matters

This approach offers a user-friendly interface to manage selections—especially good news if you’re not comfortable working with GROMACS command-line selection syntax. Saving these selections early in the preparation stage avoids mistakes and saves time later when setting up simulations or analyzing results.

Moreover, you can modify or add groups even at later stages such as minimization, equilibration, or simulation, giving you flexibility throughout your project lifecycle.

To learn more about preparing systems with GROMACS Wizard in SAMSON, visit the full tutorial: 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.

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