If you’ve ever needed to define custom index groups in GROMACS, you probably know how time-consuming it can be to manually select atoms, residues, or regions of interest using command-line tools. Whether you’re preparing systems for umbrella sampling, pulling simulations, or detailed trajectory analysis, structuring custom index groups can quickly feel like more scripting than science.
Fortunately, the GROMACS Wizard in SAMSON makes this process significantly easier — and even visually intuitive — through its custom index group interface. In this post, we’ll look at how this feature works and how it can fit seamlessly into your simulation preparation workflow.
Why Index Groups Matter
Index groups in GROMACS are used to identify specific parts of the system for further simulation steps or analysis. Common uses include calculating the distance between groups of atoms, defining pulling groups, or marking regions to apply constraints. GROMACS generates default groups (like protein, solvent, etc.), but for advanced or customized workflows, you’ll often need to define your own groups. This is where SAMSON can help.
Adding Custom Index Groups in SAMSON
From the GROMACS Wizard’s preparation stage, you can click the Add/edit index groups button to open a dialog window where you define your custom selections. Thanks to SAMSON’s powerful selection mechanisms, defining groups becomes a visual process. Use available selection tools to highlight alpha helices, N-terminal residues, or specific solvent layers, then automatically generate the GROMACS selection string.
Once selected, click Generate based on current selection in document. The wizard will construct the proper syntax for use in an index.ndx file — no need to memorize or debug selection strings manually.
Testing and Validating Your Selection
Before committing a new group, SAMSON lets you test if the selection string performs as expected. You can instantly highlight the atoms corresponding to the selection and double-check visually that the correct subset has been chosen.
Once confirmed, give the group a name (like HELICES) and append it to your simulation setup. Your index group will now be automatically incorporated into the processed system and can be reused in further steps like minimization or production runs.
When to Define Index Groups
You can define index groups at any step of your GROMACS workflow — not just in the preparation phase. However, doing it early ensures consistency and can save time if multiple steps depend on the same custom selections. SAMSON ensures these groups are incorporated into the final index.ndx file, so you don’t need to create them multiple times.
One Caveat: Unique Indices Required
To make use of custom index groups, your structure must have unique and consecutive residue and atom indices. This ensures compatibility with GROMACS indexing and prevents errors when generating the index.ndx file.
A Time-Saving Benefit for Researchers
By integrating selection, testing, and generation of index groups into a single interface, SAMSON helps streamline one of the more tedious — yet important — parts of molecular dynamics preparation. For researchers working with large systems or repeated simulations, this can mean hours saved across projects.
Learn more about preparing systems with GROMACS Wizard in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.