How to Create Custom Index Groups in GROMACS Simulations with SAMSON

If you’ve ever run GROMACS simulations, you probably know that defining the right index groups can be crucial. Whether you’re setting up pulling groups for umbrella sampling, customizing restraints, or extracting specific analysis from your trajectory, index groups give you precise control over atomic selections. But editing index.ndx files by hand? It’s tedious, error-prone, and not particularly intuitive.

Fortunately, there’s an easier way. SAMSON’s GROMACS Wizard includes a built-in tool that allows you to define custom index groups with just a few clicks—and no command-line syntax required. Here’s how it works, and why it might change how you prepare your simulations.

What Are Index Groups in GROMACS?

Index groups in GROMACS are user-defined selections of atoms that are referenced during simulations or analysis. GROMACS automatically generates standard groups (like Protein, Solvent, Ions), but complex protocols often require more specific ones—think only the alpha helices in a domain, active site residues, or ligand binding pockets.

Using SAMSON to Define Custom Index Groups

In SAMSON’s GROMACS Wizard, custom index groups can be created during the Prepare step. This allows users to benefit from SAMSON’s intuitive selection tools instead of typing atom indices or selection strings manually.

Step-by-Step: Adding an Index Group

  1. Click the Add/edit index groups button during the preparation step.
  2. A new pop-up window will appear. Here, you can manually enter a GROMACS selection string or generate one using your current selection in SAMSON.
  3. For example, select alpha helices via Select > Residues > Amino acids > Secondary structure > Alpha helices.
  4. Click Generate based on current selection in document—SAMSON automatically converts your selection into a GROMACS-compatible selection string.
  5. Name your group (e.g., HELICES) and click Add index group to the list.

Add/edit index groups

Index groups UI

Generate from selection

Index group added

Why Use SAMSON for Index Groups?

  • No syntax errors: Selections are generated automatically from your visual selections in SAMSON.
  • Speed: No need to look up atom numbers or remember GROMACS syntax—you just select what you see.
  • Reusability: Once created, custom groups are stored in the standard index.ndx and can be reused at later steps (minimization, equilibration, production).

Tips

  • Make sure your system has unique and consecutive residue and atom indices before creating custom groups.
  • You can define multiple groups at this stage and update them later in the workflow.

This integration of visual selection and automatic index group generation is a small but powerful feature. It’s especially helpful if you often work with large biomolecular systems, or need to create multiple custom selections repeatedly.

To learn more about the full preparation workflow in GROMACS Wizard, visit the original documentation page.

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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