Avoiding Pitfalls When Adding Custom Index Groups in GROMACS Wizard

If you’re running molecular dynamics with GROMACS and customizing index groups for your simulations, you might have encountered some unexpected behavior—especially when defining groups too early in the workflow. While platforms like SAMSON make setup much smoother, there’s a subtle but important consideration: when to add your custom index groups during system preparation, equilibration, and simulation can significantly affect your results.

What’s the Problem?

GROMACS has an automatic way of generating standard index groups—like Protein, Water, and Ion—based on your molecular system. These groups are useful for analysis, restraints, or pulling during simulations. But often, you need custom groups: a set of alpha carbons, a subset of sidechains, or a selection based on charged residues. Knowing how to safely add these groups without causing indexing issues is key—especially if you’re using batch processing or complex systems.

Why Timing Matters

The GROMACS Wizard in SAMSON lets you add custom index groups at any point, but it’s important to understand the trade-offs of doing this at the Preparation step vs the later Equilibration or Simulation steps:

  • Preparation step: Suitable for batch processing since groups are applied once and reused across sub-projects. However, default index groups from GROMACS aren’t yet created at this stage, so you can’t build custom selections that depend on them.
  • Equilibration/Simulation step: Ideal if you want to build on existing default groups. You can freely reference GROMACS-generated groups like Protein in your custom selection strings.

Warning

If your system has non-unique or non-consecutive indices for atoms or residues, adding index groups at the preparation step can lead to unexpected indexing issues. Always validate your selections afterward.

Best Practice: Add Custom Index Groups After Preparation

To reduce indexing issues and increase flexibility, many users benefit from waiting until the Equilibration or Simulation step. Here, the index file (index.ndx) already contains the standard groups, making it easier to build complex selection strings.

Steps to Add Custom Index Groups in Equilibration/Simulation

  1. Ensure the system is loaded in SAMSON. If not, click Load.
  2. Click the Edit index groups button.
  3. In the GROMACS Index Groups window, browse the existing default groups. You can’t modify them, but you can use their names in selection strings.
  4. Either:
    • Use a GROMACS-style selection string (e.g., "Protein" & ! "C-alpha").
    • Or, use SAMSON’s selection tools to graphically select atoms or residues, and click Generate based on current selection to auto-generate the selection string.
  5. Name your new custom group and click Add index group to the list.
  6. Click Apply to save to index.ndx.

This approach reduces errors and allows you to build on what GROMACS already knows about your system.

Add a custom index group

Final Tips

  • Always test your selection strings using the Test selection string button.
  • Use Select in document based on selection string to visualize the exact atoms or residues before adding the group.

Getting your custom index groups just right requires some care—but SAMSON makes it easier to avoid pitfalls and validate your selection before launching time-consuming MD runs.

To learn more, visit the official documentation page: https://documentation.samson-connect.net/tutorials/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.

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