Custom Index Groups: Fine-Tune Your Simulation Setup in SAMSON

When preparing molecular simulations with GROMACS, setting up your system with precision can save you from troubleshooting downstream. One common pain point for molecular modelers, particularly when dealing with analysis or advanced simulation protocols like umbrella sampling and pulling experiments, is the need to define custom index groups.

While GROMACS automatically creates standard index groups (e.g., protein, solvent, ions), these may not always align with your scientific question. For example, you might want to focus on a specific domain of a protein, hydrophobic residues, or a particular secondary structure like α-helices. Creating custom index groups is essential in these scenarios—and that’s where SAMSON’s GROMACS Wizard can help.

What Are Index Groups?

In GROMACS, index groups are used to define collections of atoms for use in a wide array of simulation steps: from calculating distances and RMSD, to applying restraints and defining pull groups.

Why Create Custom Index Groups?

  • Define regions of interest (like active sites or binding pockets)
  • Use specific atom groups for umbrella sampling or steered MD
  • Enable more targeted analysis post-simulation

How to Create Custom Index Groups in SAMSON

The process is integrated seamlessly into the GROMACS Wizard’s preparation step. Here’s a step-by-step example using α-helices as a target structure:

  1. In SAMSON, perform a selection using the Visual interface: Select > Residues > Amino acids > Secondary structure > Alpha helices.
  2. Click on Add/edit index groups.
  3. In the pop-up, press Generate based on current selection in document.
  4. Name your group (e.g., HELICES).
  5. Click Add index group to the list.

Generate an index group selection string based on the current selection in the document

That’s it. SAMSON automatically converts your selection into GROMACS-compatible syntax, stores it in an index.ndx file via gmx make_ndx, and saves it in the project folder.

Other Notable Features

  • You can continue adding new index groups later during minimization, equilibration, or production runs.
  • If your system has well-defined atom and residue indices, SAMSON ensures compatibility with GROMACS conventions.

This simple yet powerful workflow helps eliminate ambiguity during simulations and enhances reproducibility. It’s especially useful for users performing complex simulations like protein-ligand binding studies or unfolding simulations.

Learn more about creating index groups and other preparation steps in the full documentation: GROMACS Wizard Prepare Step.

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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