When working with molecular simulations in GROMACS, little is more frustrating than realizing — mid-way through equilibration — that you forgot to define a group of atoms you need for a specific analysis or biasing method. And while GROMACS automatically provides index groups like protein, water, and ions, your simulation might require more specific ones.
That’s where custom index groups come into play — and planning their creation early in the workflow can save time, hassle, and errors later on. In this post, we explore how to define these custom groups during the preparation step using the GROMACS Wizard in SAMSON, allowing you to reuse them consistently across all future simulation stages.
Why create custom index groups early?
Index groups are essential in GROMACS for tasks such as pulling, restraining, or simply monitoring specific parts of your system (e.g., a loop region, binding site, or ligand). Defining these groups as early as possible, especially in a batch project involving multiple subprojects, ensures consistency and reduces human error. More importantly, it means you avoid repeating the same setup steps later for each subproject individually.
Using the GROMACS Wizard in SAMSON, you can create these custom groups during preparation thanks to advanced selection tools — either by typing selection strings or interactively selecting atoms, residues, or molecules in the document.
How it works in SAMSON
In your single or batch simulation project:
- Select atoms or molecules using SAMSON’s visual interface, including filters like
Select > Residues > Amino acids > Side chain charge > Neutral. - Click the Edit index groups button in the GROMACS Wizard interface to open the Index Groups window.
- Click the + button to create a new group, and then use Generate based on current selection in document.
- Name your group and click Add index group to the list, then Apply.
This will save your group to the index.ndx file, which is automatically used by GROMACS during subsequent steps.
Limitations to keep in mind
One thing to note: At the preparation step, default GROMACS index groups are typically not yet available. This means that you can’t reference them in your selection strings at this stage. You’ll need to rely on either direct selection in SAMSON or define entirely new groups using explicit atom/residue criteria.
Also, if your system includes atoms or residues with non-unique or non-consecutive indices, indexing might not behave as expected. Always verify the resulting groupings to make sure they match your intention.
Better batch workflow through early planning
For single-project simulations, you have more flexibility to define index groups during equilibration or simulation. But in batch mode, where consistency is key, setting these up early avoids duplication and reduces mistakes.
If you use a frequently needed group (e.g., all backbone atoms or a ligand binding pocket), creating it during preparation helps enforce standardization across your data — which is especially helpful for automation and reproducibility.
To learn more, check out the full documentation page on Adding Custom Index Groups in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here: https://www.samson-connect.net.