When preparing molecular simulations in GROMACS, one common need among computational researchers is the ability to define precise groups of atoms or residues—whether for analysis, distance restraints, pull groups, or umbrella sampling setups. While GROMACS offers native tools like gmx make_ndx for creating index groups, it can be tricky to define complex selections without a visual aid. Here’s where the GROMACS Wizard in SAMSON brings an elegant, user-friendly solution. 🧪
In this blog post, we explore the optional but powerful feature of adding custom index groups to your GROMACS project directly from within SAMSON, using its visually-driven selection interface and automated syntax generation. This capability makes it much easier to define specific structures like secondary elements, binding pockets, or ligand groups—without the guesswork.
Why You Might Want Custom Index Groups
By default, GROMACS generates standard index groups—protein, non-protein, solvent, ions, etc. But what if you need to:
- Track a specific helix during a simulation?
- Apply restraints to a ligand?
- Define a dynamic region of interest for analysis?
For this, creating your own index groups becomes essential.
How It Works in SAMSON
Here’s how you can define custom index groups in SAMSON, integrated into the GROMACS Wizard workflow.
1. Launch the Index Group Editor
Following system selection in the Prepare step, click the Add/edit index groups button:
2. Select Atoms or Residues Visually
Rather than typing a command-line expression, use SAMSON’s visual selection tools. For example, to select all residues in alpha helices, go to:
Select > Residues > Amino acids > Secondary structure > Alpha helices.
3. Automatically Generate the Selection String
Once you’ve made your selection, click the Generate based on current selection in document button. SAMSON translates your visual selection into a GROMACS-compatible selection string (e.g., r 5 & a CA).
4. Name and Add Your Group
Give your group a meaningful name, like HELICES, test it if needed, then click Add index group to the list.
Your newly added group will appear in the list of custom index groups:
What Happens Next?
These definitions are saved in the index.ndx file and will persist throughout the simulation setup, minimization, and even production run steps. You can also reuse or modify them later in the workflow.
Reminder: To use this feature, your structure must have consecutive and unique atomic and residue indices.
This painless index group builder is especially useful when dealing with complex systems or preparing for enhanced sampling techniques like umbrella sampling, pulling, or contact-based constraints.
To learn more and explore other advanced preparation features, visit the complete tutorial on GROMACS Wizard – Step 1: Prepare.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.