How to Create Custom Index Groups in GROMACS Wizard Without Writing a Line of Code

When running advanced molecular dynamics simulations, especially those involving pull groups or complex post-simulation analysis, it’s often necessary to define custom index groups. This is typically done using gmx make_ndx, which requires knowledge of GROMACS command-line syntax and selection strings.

But if you’re using SAMSON’s GROMACS Wizard, you don’t need to touch the command line at all. The wizard provides a graphical interface to create custom index groups using intuitive selection tools. You can visually pick the parts of your system you need, and let SAMSON generate the GROMACS-compliant selection strings for you. Here’s a step-by-step look at how it works inside the GROMACS Wizard.

When and Why Would You Need a Custom Index Group?

By default, GROMACS generates standard index groups like whole proteins, solvent, and ions. But sometimes you want more control, for example:

  • Pulling only alpha-helix residues in a simulation
  • Analyzing flexible loop regions separately
  • Tracking non-standard ligands or co-factors separately

In such cases, custom groups let you define selections that can be reused across simulation stages.

How to Do It in SAMSON

Once you’ve chosen your molecular system in the GROMACS Wizard and reached the “Prepare” stage, you can set up custom index groups like this:

  1. Click the Add/edit index groups button.
  2. A window will pop up that allows you to add index groups visually or using selection strings.
  3. Use SAMSON’s selecting tools from the menu bar (e.g., Select > Residues > Amino acids > Secondary structure > Alpha helices).
  4. Click Generate based on current selection in document—SAMSON will translate your visual selection into a GROMACS selection string.

Select alpha helices

Generate an index group selection string

Then:

  • Give the group a name (e.g., HELICES)
  • Optionally test the selection by highlighting associated atoms
  • Click Add index group to the list

Add index group

Tips and Considerations

  • Index groups are saved in the index.ndx file using the gmx make_ndx command under the hood.
  • This step is optional, but can be carried out during later stages like minimization or simulation as well.
  • The selected system should have unique and consecutive indices for atoms and residues for consistency with GROMACS conventions.

Finally, once the system is prepared and imported back into SAMSON, the custom groups appear as independent selectable items inside the Document View. You can double-click them to instantly visualize or manipulate the associated atoms or residues.

Index groups in document

A Flexible Solution for Complex Projects

With batch projects and large trajectories, custom index groups can also be carried over into umbrella sampling, RMSD calculations, or distance monitoring. Defining them early in a reliable and visual way can save time and reduce ambiguity in naming and selection consistency.

To learn more about other features in the preparation step, visit the full documentation page: GROMACS Wizard – Step 1: Prepare.

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

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