Anyone working with molecular dynamics (MD) simulations knows the pain: you’re ready to analyze some subtle motion or apply restraints during your GROMACS run, and the default index groups just won’t cut it. You need something specific — a pocket, a patch of residues, or perhaps a handful of atoms responding to an external force. But editing GROMACS index files manually is slow, error-prone, and not very intuitive.
If you’ve felt this frustration, here’s the good news: the GROMACS Wizard in SAMSON gives you a much easier way to add custom index groups using either GROMACS selection syntax or SAMSON’s user-friendly selection tools. It’s fast, visual, and integrated into your workflow.
What Are Index Groups and Why Customize Them?
Index groups in GROMACS define subsets of atoms and are used for everything from restraints to analyses. GROMACS provides default groups like Protein, Water, or Backbone, but these are often too general for advanced work.
Need to track just the side chains of neutral amino acids? Pull only the alpha carbons of a domain? You’ll need your own index groups. With GROMACS Wizard in SAMSON, creating those becomes much easier — and visual.
How It Works in SAMSON
Once your system is prepared in SAMSON, just head to the equilibration or simulation steps in the GROMACS Wizard and load your project (if not already loaded).
From there, click on Edit index groups:
A list of automatically generated GROMACS groups appears. You can explore these, but not modify them. However, you can use them in new combinations to create your own groups — powerful!
Create a Group Using Existing Index Groups
Let’s say you want to exclude alpha-carbons from a protein for a pulling experiment. You can do this with a simple logic string:
"Protein" & ! "C-alpha"
You can test this string, visualize the selection in SAMSON, and verify that it’s selecting exactly what you want, visually and interactively.
Or Select Graphically Inside the 3D Editor
Prefer visual interactions? SAMSON lets you create a group by selecting atoms/residues directly in your model. For example, you can choose neutral-charged residues via a few menu clicks:
Select > Residues > Amino acids > Side chain charge > Neutral
Then click Generate based on current selection in document to automatically convert the selection into a GROMACS-compatible selection string. No typos, no atom ID headaches.
Finally, click Add index group to the list and then Apply to save. Your new group is now written directly into your project’s index.ndx file — and you’re ready to simulate or analyze!
Final Tip
If you’re working on multiple systems or a high-throughput setup, it’s better to define these custom index groups during the preparation step. This ensures the same groups are propagated consistently across all simulations.
Whether you’re running free energy calculations, pulling simulations, or just need precise analysis, custom index groups are the key to clarity. And with SAMSON’s GROMACS Wizard, setting them up is simple and visual.
To learn more, visit the original tutorial page: GROMACS Wizard – Adding custom index groups.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.