One often overlooked feature when preparing molecular simulations in GROMACS is the ability to define custom index groups. These user-defined selections can make a big difference in trajectory analysis, pulling simulations, and restraint settings. If you’ve ever found yourself wishing that you could quickly refer to a specific set of residues or atoms during a simulation, this post is for you.
In GROMACS Wizard for SAMSON, adding such index groups is simple and integrates seamlessly into the preparation workflow. You don’t need to worry about manually editing index.ndx files or wrangling with selection strings—you can leverage SAMSON’s interactive selection tools to define your group visually, and the tool generates the rest.
Why define custom index groups?
GROMACS automatically creates default index groups such as Protein, Solvent, NA, and CL. However, in many advanced setups like umbrella sampling, you may need specific groups, e.g., only the alpha helix of a protein, ligand atoms, or atoms involved in specific interactions.
Instead of later modifying index files by hand, it’s better practice to specify these custom groups right during the preparation stage using the Add/edit index groups button:
How it works in SAMSON
Clicking the Add/edit index groups button opens a window for defining new groups. You can input GROMACS selection strings manually or generate them based on current selections in the SAMSON interface.
As an example, suppose you want to define a group containing all residues in alpha helices. You can use SAMSON’s selection menu: Select > Residues > Amino acids > Secondary structure > Alpha helices. Once selected, click the Generate based on current selection in document button to let GROMACS Wizard complete the GROMACS-compatible syntax for you.
After creation, click Add index group to the list and give it a name (for instance, HELICES):
Once registered, the new group is shown in the list, and when simulation results are loaded back in SAMSON, you can interactively select it again using the Document view.
Requirements and tips
- Make sure residue and atom indices are unique and sequential.
- Custom index groups are saved in the
index.ndxfile. - You can still define or edit custom groups later—in the minimization, equilibration, or production stages.
This feature may seem minor, but if you’re running complex workflows or want to simplify downstream analysis, defining your own index groups early on can save time and provide clarity.
To learn more about preparing systems and index groups with GROMACS Wizard in SAMSON, visit the full guide: https://documentation.samson-connect.net/tutorials/gromacs-wizard/preparation/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.