When setting up molecular simulations in GROMACS, automated tools do a great job generating standard index groups (like protein, water, ions). But often, researchers need more control: you might want to monitor a specific subset of amino acids, calculate distances between a ligand and binding site, or apply pulling forces during simulations. This is where custom index groups come into play.
In SAMSON’s GROMACS Wizard, defining custom index groups is simple and can be a powerful time-saver. This post walks you through why and how to create these groups, focusing on real-world use cases and customization options.
Why Custom Index Groups Matter
GROMACS uses index groups in many contexts: to apply position restraints, pull constraints, define analysis selections, etc. If you’re tracking specific residues or non-standard selections (e.g., hydrophobic pocket residues, loop regions, or ligands), relying solely on default groups won’t be enough.
Instead of editing .ndx files manually, which can be error-prone and tedious, you can use SAMSON’s built-in group editor to do this visually—saving time and reducing the risk of mistakes.
How to Add Custom Index Groups in SAMSON
Once you’ve selected your system for preparation, follow these steps to create custom index groups:
- Click the Add/edit index groups button.
- Select atoms or residues directly in the SAMSON GUI using intuitive selection filters (e.g., by secondary structure or residue name).
- Click Generate based on current selection in document. This automatically creates the GROMACS-compatible selection string.
- Name the group (e.g.,
HELICES), test it if needed, and click Add index group to the list.
Once added, custom groups are saved in the index.ndx file and can be used across multiple steps: energy minimization, equilibration, and production runs.
Example: Identifying Alpha Helices
Say you want to define a group for alpha helical residues in a protein. Simply go to Select > Residues > Amino acids > Secondary structure > Alpha helices in SAMSON’s selection menu.
Then generate the equivalent GROMACS string and register the group. This is immensely helpful if, for instance, you want to compute RMSD over only the helical regions or apply restraints specifically there.
Tips and Recommendations
- Ensure consistent residue and atom indices: Custom groups require unique and consecutive indices — typical in well-prepared systems.
- No need to repeat in later stages: Once defined, these groups persist and can be reused in minimization or simulation stages.
- Combine with automated tools: Use GROMACS Wizard’s automation but fine-tune with your domain-specific selections for richer analyses.
Conclusion
Whether you’re running protein-ligand simulations or studying conformational changes, custom index groups streamline setup and make complex selections reliable and reproducible. Instead of managing selections via command-line tools or editing configuration files by hand, visualize and define them directly within SAMSON—making the workflow cleaner and easier to manage.
To learn more about system preparation and custom index groups in SAMSON’s GROMACS Wizard, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.