Custom index groups can be extremely helpful in molecular dynamics simulations, especially when performing detailed analyses or steering parts of your system through advanced scenarios like umbrella sampling or pulling simulations.
However, defining these groups using command-line tools and selection scripts can be intimidating—even frustrating—for researchers who would rather focus on the science than the syntax.
If you’re using SAMSON’s GROMACS Wizard, the good news is: you don’t need to write selection commands manually. Instead, you can visually select atoms or residues using intuitive tools and have GROMACS-compatible selection strings generated for you.
Why use custom index groups?
GROMACS automatically creates default index groups such as Protein, Water, and Ion, but there are many cases where you need more tailored groups, such as:
- Tracking movement of specific helices or domains
- Defining pulling groups for steered MD simulations
- Calculating distances between two functional sites
- Restraining specific atoms during equilibration
SAMSON simplifies this by letting you create groups using visual selections, which can be based on structural features like secondary structure elements or custom-defined regions.
Step-by-step: Visually define custom index groups
- After choosing your system in SAMSON’s GROMACS Wizard interface, locate and click the Add/edit index groups button.
- A new pop-up window opens where you can either type a GROMACS selection string or generate one automatically based on your current selection in the 3D document view.
- For example, to select all residues that are alpha helices, use the interface to go to Select > Residues > Amino acids > Secondary structure > Alpha helices.
- Click the Generate based on current selection in document button. This will auto-generate a valid GROMACS selection string.
- Give your group a name (e.g.
HELICES) and click Add index group to the list.
The group is now ready and will be included in your index.ndx file. You’ll be able to use it in any future steps (minimization, equilibration, production) or in analysis tasks.
Key advantages
- No command-line syntax: Just point and click.
- Reusable: Custom groups are added to the GROMACS index file and available later.
- Error-reduction: Selection strings are generated automatically from proper selections.
- Integration: SAMSON uses its internal selection mechanisms, offering options that go beyond simple atom names or residue ranges.
Requirements
Make sure your system has unique and consecutive atom and residue indices. If this is not the case, GROMACS may produce errors when the index file is used.
To learn more about this and other features in the preparation phase, visit the official documentation page: GROMACS Wizard – Preparation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at https://www.samson-connect.net.