Custom Index Groups in GROMACS: A Simple Way to Target Specific Atoms and Residues

If you’ve ever run a molecular dynamics simulation using GROMACS, there’s a good chance you’ve faced this frustrating moment: you need to track say, only the side chains of neutral residues, or analyze specific atoms across your trajectory — but the default index groups generated by GROMACS don’t quite cover what you need. 🤯

That’s where the GROMACS Wizard in SAMSON offers a helpful solution: custom index groups. This feature allows you to define exactly the sets of atoms or residues you care about, using either the powerful GROMACS selection syntax or a visual selection in SAMSON.

Let’s walk through how to do this during the equilibration or simulation steps of your molecular modeling workflow—ideal stages since all standard groups are already generated and ready to be referenced.

Step 1: Load Your System

If it’s not already loaded, simply click the Load button next to the input path. Your system must be loaded in SAMSON to allow editing of index groups.

Step 2: Open the Index Group Editor

Click the Edit index groups button. You’ll see the GROMACS Index Groups window, which includes a list of default groups.

Default index groups

Step 3: Define a New Group

You have two powerful options here:

  • Use the GROMACS syntax directly. For example:
    This example selects all non-C-alpha atoms in the protein.
  • Use interactive selection in SAMSON. Select nodes visually (for instance, all amino acids with neutral side chain charges via Select > Residues > Amino acids > Side chain charge > Neutral) and generate the corresponding GROMACS selection string.

Select amino acids with neutral side chains

Once selected, click + under the group list, then click Generate based on current selection in document. Give your new group a name, click Add index group to the list and hit Apply. SAMSON will handle writing everything to the index.ndx file for you.

Creating a custom index group

Why this Matters

Custom index groups are essential when your analysis or simulations require tailored atom selections—like comparing backbone rigidity between charged and neutral residues, or monitoring specific functional sites.

With SAMSON, you skip the error-prone manual editing often needed when using gmx make_ndx in a terminal, speeding up your workflow and reducing the chance of mistakes.

To learn more about how to manage custom index groups in other steps (like preparation) or issues related to atom indexing, check out the full documentation at this link.

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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