When setting up molecular dynamics simulations in GROMACS, it’s often useful—if not essential—to define specific groups of atoms for analysis and specialized operations (e.g., as pull groups or monitoring specific domains). These are known as index groups. While GROMACS can generate predefined index groups (like Protein, SOL, etc.), the ability to create custom index groups gives molecular modelers more flexibility and control.
However, defining custom index groups manually with selection strings in the traditional GROMACS interface can be tedious and error-prone, especially in larger systems or batch operations. Fortunately, the GROMACS Wizard in SAMSON simplifies this through an intuitive GUI and powerful selection tools.
Why Custom Index Groups Matter
Custom index groups allow you to:
- Track specific regions of a protein (e.g., an active site or loop region)
- Define pull groups for umbrella sampling or steered MD
- Isolate ligand or cofactor behavior
- Compare residue domains across different conformations
But perhaps most commonly, users want to create groups like “alpha-helical residues” or “binding site atoms” efficiently. That’s where SAMSON shines.
How It Works in SAMSON
After setting your system in the GROMACS Wizard, you can add custom index groups by clicking the Add/edit index groups button:
This opens a new window designed for group creation. You can either:
- Manually input a GROMACS selection string, or
- Use the SAMSON selection UI to pick atoms visually or by property—SAMSON then generates the selection string for you.
Example: Select Alpha Helices
1. Use SAMSON’s menu: Select > Residues > Amino acids > Secondary structure > Alpha helices.
2. Back in the Index Groups window, click Generate based on current selection in document:
3. Give your group a name, such as HELICES, then click Add index group to the list:
4. Your new group appears ready for use:
Technical Notes
- New groups are saved to
index.ndxusinggmx make_ndx. - A prerequisite is that atoms and residues must have unique, consecutive indices.
- You can create additional groups later in minimization, equilibration, or production steps.
When to Use This
Anytime you need granularity. This could be for sampling subsets of a protein, tracking dynamics of ligands, or defining pull vectors in free energy calculations. Compared to editing index files manually, the SAMSON approach is visual, fast, and less prone to mistakes.
To learn more about this feature and other preparation steps, visit the full GROMACS Wizard documentation page here: GROMACS Wizard – Preparation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net