When setting up a molecular system for simulation in GROMACS, atom group selections—known as index groups—play an important role in defining regions for restraints, analysis, and advanced sampling techniques like umbrella sampling. While GROMACS automatically generates standard index groups (e.g., Protein, SOL, NA), researchers often need to define custom groups. For instance, you might want to track only alpha helices, a group of active site residues, or an interface between two domains.
But here’s the catch: Traditional workflows for creating custom index groups require manual scripting using gmx make_ndx with GROMACS selection syntax. This can quickly become tedious and error-prone, especially when dealing with large systems or many custom selections.
SAMSON’s GROMACS Wizard provides an intuitive visual solution. By using SAMSON’s rich selection mechanism and graphical interface, you can quickly define custom index groups—without writing a single line of code.
Adding Custom Index Groups the Easy Way
Below is a step-by-step overview of how to use SAMSON to define and manage custom index groups for your systems:
- Set your system in SAMSON using the GROMACS Wizard’s preparation workflow.
- Click the Add/edit index groups button.
This opens a pop-up window tailored for managing index groups. Here’s where SAMSON’s user interface makes things easier.
Example: Selecting Alpha Helices
You can use the selection menu: Select > Residues > Amino acids > Secondary structure > Alpha helices to visually highlight alpha helices in your protein.
Then, within the Index Groups window, click on Generate based on current selection in document.
Give your new group a name (such as HELICES), and you can even test the selection expression. Once you’re satisfied, click Add index group to the list.
The new group appears in your groups list:
Why This Matters
- Enables easier setup for advanced sampling techniques, such as umbrella sampling or steered MD.
- Saves time by avoiding manual syntax entry and selection retries.
- Improves reproducibility: your custom selections are saved and connected with the system setup.
- Less prone to errors thanks to a visual interface and automated coordinate extraction.
Tip: These groups are stored in the index.ndx file and can be reused in subsequent GROMACS stages (minimization, equilibration, production).
Summary
This approach offers a much-needed solution to one of the more cumbersome parts of simulation setup: identifying and encoding custom selections. Whether you’re isolating flexible loops or charged side chains, SAMSON’s integration with GROMACS takes the guesswork (and keyboard work) out of the equation.
To dive deeper into the preparation process, including batch setups and solvent/force field configuration, read the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.