When running GROMACS simulations, defining custom selection groups—also known as index groups—can be essential. These groups allow for targeted analysis, pulling configurations, and interaction computations. However, editing GROMACS .ndx files manually is tedious and error-prone, especially when dealing with large biomolecular systems.
With the GROMACS Wizard in SAMSON, you can populate index groups visually and automatically from selections, without manually typing atom numbers or crafting special syntax. This simplifies workflows for researchers and improves reproducibility.
What Problem Are We Solving?
In standard GROMACS usage, defining custom index groups often requires using gmx make_ndx interactively, or manually crafting .ndx files. That can be painful:
- You’ll need to know the exact atom/residue numbers.
- Group definitions are hard to debug.
- Visualizing what you’re selecting isn’t straightforward.
Instead, SAMSON’s GROMACS Wizard enables point-and-click selection of atoms using highly flexible filtering, and generates GROMACS-compatible selection strings automatically.
Creating Custom Index Groups Visually
Step-by-step:
- Open the Preparation step in the GROMACS Wizard.
- Once your molecular system is set, click the Add/edit index groups button.
This launches a pop-up interface for defining custom index groups.
Selecting Atoms in the Viewport
Use the main viewport to define your selection. For example, to select all alpha helices:
- Go to Select > Residues > Amino acids > Secondary structure > Alpha helices.
- Click Generate based on current selection in document.
GROMACS-compatible selection strings are generated automatically. Then, you can name the group (e.g. HELICES) and click Add index group to the list.
The group appears in the list of index groups:
How It Works Under the Hood
These groups are injected into the preparation workflow via the gmx make_ndx command. SAMSON automatically creates the correct syntax and saves the index group in the generated index.ndx file within your project folder. Even better, this step supports GROMACS syntax as well as SAMSON’s own rich selection interface.
Why Use Custom Groups?
Custom index groups can be used:
- As pull groups in steered molecular dynamics.
- To track specific domains or residues over time.
- For focused energy contributions or distance monitoring.
And you don’t need to define them all at once—additional groups can be added during the Minimization, Equilibration, or Simulation steps later.
Tips
- Residue and atom indices must be unique and consecutive for successful creation.
- You can also test the selection string to ensure it behaves as expected.
This level of flexibility is a great way to make your simulations more tailored without losing time in the terminal.
To learn more, check out the GROMACS Wizard Preparation documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/preparation/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.