Why Add Custom Index Groups in GROMACS—and How to Do It Easily in SAMSON

One of the small but persistent frustrations when working with GROMACS is managing index groups—especially when preparing for analyses that require specific selections such as pull groups, regions of interest, or structural motifs like alpha helices. Default index groups are helpful, but custom index groups give you the flexibility needed for more consistent, automated analysis pipelines.

If you’ve ever opened a index.ndx file and manually typed in atom ranges, you know how error-prone and tedious this process can be. Especially when dealing with larger systems or multiple frames in a trajectory. Fortunately, this is where the GROMACS Wizard in SAMSON really helps.

Why Custom Index Groups Matter

GROMACS generates standard index groups based on system components—protein, solvent, ions, etc. However, simulations often require more specific selections. For instance:

  • Selecting only alpha helices or beta sheets for RMSD analysis
  • Defining a subgroup of atoms to apply pulling forces
  • Tracking ligand movement relative to a particular binding pocket

Adding these groups manually outside of SAMSON can be cumbersome and hard to reproduce—especially in batch simulations. But with SAMSON’s visual selection tools embedded in the GROMACS Wizard, this becomes much easier.

How to Add Custom Index Groups in SAMSON

Step 1: After choosing your molecular system for preparation in the GROMACS Wizard, click the button labeled Add/edit index groups.

Add/edit index groups

Step 2: A pop-up dialog will appear. You can now specify new index groups either by writing a GROMACS selection string manually, or even better—by visually selecting atoms or residues in SAMSON.

Index groups UI

Step 3: For example, to select alpha helices, go to the menu: Select > Residues > Amino acids > Secondary structure > Alpha helices. Once selected, click the Generate based on current selection in document button.

Select alpha helices

Generate an index group selection string based on the current selection

Step 4: Give your new group a name (e.g., HELICES) and click Add index group to the list.

Add the index group

A newly added index group

Best Practices & Tips

  • Residue and Atom Indexing: Make sure atom and residue indices are unique and consecutive for index groups to work properly.
  • Reuse in Later Steps: Custom index groups aren’t limited to preparation. You can reuse or add new ones in the minimization, equilibration, or simulation stages.
  • Consistency Across Batches: When working with batch simulations or multiple states of the same molecule, predefined index groups help keep everything consistent, especially in automated workflows.

Conclusion

Adding custom index groups doesn’t have to be manual or restricted to post-processing. With SAMSON’s GROMACS Wizard, you can visually define and validate these groups right at the system preparation stage—saving time and reducing errors.

To learn more about preparing molecular systems and customizing simulations in SAMSON, visit the full documentation: GROMACS Wizard – Prepare.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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