Creating Custom Index Groups in SAMSON for Smarter GROMACS Simulations

When running molecular simulations with GROMACS, organizing parts of your system into logical groups can make a huge difference in analysis and setup—especially if you need to define regions of interest like specific residues or structural motifs. In GROMACS terminology, these are called index groups. Fortunately, the SAMSON GROMACS Wizard makes defining custom index groups much simpler and more visual than using command-line tools alone.

Whether you’re preparing a protein–ligand complex, setting up umbrella sampling, or analyzing simulation results, knowing how to create well-defined index groups in advance can save a lot of frustration.

Why and When to Add Custom Index Groups?

GROMACS automatically creates standard groups like Protein, Water, or Ion, but sometimes you need more:

  • To define pull groups for free energy calculations
  • To analyze specific secondary structures such as helices or beta sheets
  • To select a ligand or pocket region

Such custom groups are usually defined manually using gmx make_ndx, a command-line utility. SAMSON simplifies this process significantly with interactive tools and automatic generation of selection strings.

How to Create Custom Index Groups in SAMSON

Here’s how to add a custom index group using the SAMSON GROMACS Wizard:

  1. Prepare and validate your system in the document view.
    You can select the molecular system or conformation set just like you would when starting a simulation.
  2. Click the Add/edit index groups button:
    Add/edit inde groups
  3. Use the SAMSON interface to make a selection you’re interested in. For example, select all residues in alpha helices:
    Select alpha helices
  4. In the index group dialog, generate a selection based on the current selection in the document:
    Generate an index group selection string based on the current selection in the document
  5. Name your group (e.g., HELICES), test, and click Add index group to the list.
    Add the index group to the list
  6. The new group will now be part of your project and saved in the index.ndx file.
    A newly added index group in the list

Best Practices

  • Only add index groups after the system has unique and consecutive residue and atom indices.
  • These groups can be reused in later stages (minimization, simulation, analysis, etc.).
  • Use clear names for index groups to avoid confusion later on.

Adding informative, custom index groups can make analyses (like RMSD, distance monitoring, or pulling experiments) smoother and more meaningful. By leveraging SAMSON’s visual interface and automatic selection conversion, you can work smarter—not harder.

To dive deeper into adding custom index groups and other setup options, visit the official SAMSON GROMACS Wizard Preparation tutorial.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON here.

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