Save Time During Analysis: Add Custom GROMACS Index Groups with a Click in SAMSON

When working with molecular dynamics in GROMACS, a common challenge for researchers is identifying and selecting specific parts of the system repeatedly during setup or analysis. Whether you’re analyzing motion in alpha helices, tracking ions, or applying restraints, you often need custom index groups to save time and maintain consistency throughout your simulations.

Traditionally, creating these custom groups involves manually writing selection syntax in gmx make_ndx. This can be error-prone, particularly when dealing with large or complex systems. The SAMSON GROMACS Wizard provides a visual, user-friendly alternative that simplifies this process significantly.

Why Index Groups Matter

Index groups are fundamental to many GROMACS workflows. They let you:

  • Apply position restraints to specific residues.
  • Calculate RMSDs for subsets of atoms.
  • Define pull groups for steered MD or umbrella sampling.
  • Monitor hydrogen bonds or distances within custom regions.

But defining these precisely—especially when based on structural features like secondary structure—often requires mapping residue numbers or atom names and checking them twice. SAMSON removes this friction.

From Visual Selection to Ready-to-Use Groups

Here’s how you can define custom GROMACS index groups in SAMSON without having to think about atom indices or GROMACS syntax:

  1. After loading your system, use SAMSON’s Select menu: for example Select > Residues > Amino acids > Secondary structure > Alpha helices.
  2. Click on Add/edit index groups in the GROMACS Wizard.
  3. In the pop-up window, click Generate based on current selection in document.
  4. Name the new index group (e.g., HELICES).
  5. Optionally, test the selection visually to confirm it’s correct.
  6. Click Add index group to the list.

The selection string is generated automatically and stored in the index.ndx file. You can reuse it in later steps like minimization, equilibration, or production simulations.

Add the index group to the list

Need an Example?

Let’s say you want to track how alpha helices behave during the simulation. Instead of identifying which residues correspond to helices and manually writing the selection string, you just select them through the visual menu, name the group, and you’re done. As a result, your group HELICES is now part of index.ndx, linked directly to your structure.

You can create as many custom groups as needed—fragments, surfaces, ligands—anything you can select visually in SAMSON, you can turn into an index group.

Things to Keep in Mind

  • Your atoms and residues should have unique, consecutive indices for this to work smoothly.
  • Standard index groups are still generated automatically, and you can combine them with your custom groups.
  • You can modify or add additional groups in future stages if needed.

To learn more about the other capabilities of preparation in the GROMACS Wizard (like batch projects, solvent models, or force fields), visit the full documentation page at this link.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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