A Simple Way to Create Custom GROMACS Index Groups in SAMSON

For many molecular modelers working with GROMACS, defining custom index groups is a familiar but often tedious task. Whether you’re preparing complex systems or performing steered molecular dynamics, accurate grouping of atoms, residues, or chains is essential. One particularly common use case is selecting specific chains for pulling simulations or restraints in production MD. Typically, you’d need to use command-line tools like make_ndx to define your groups, often requiring lengthy typing or careful syntax. But what if you could do all of this visually and interactively?

In this post, we’ll explore how SAMSON’s GROMACS Wizard simplifies the creation of custom index groups using its interactive Graphical User Interface. We’ll focus on a practical example: defining two chains (A and B) of the 2BEG protein system to perform center-of-mass pulling.

Why Custom Index Groups Matter

GROMACS comes with default groups like ‘Protein’, ‘Water’, and ‘Ions’. However, in many simulations — like pulling, umbrella sampling, or selective restraints — you often need finer control. Defining a group for a specific chain or even a subset of atoms allows you to apply forces or restraints precisely where they are needed, improving both the accuracy and efficiency of your simulations.

Visual Selection in SAMSON

In SAMSON, custom index groups can be easily created directly from the molecular visualization interface. Here’s how:

  1. Use the Document view to locate and select a specific chain. For example, select chain A from the 2BEG structure.
  2. Click the Edit index groups button in the Simulate tab of GROMACS Wizard.
  3. Click Generate based on current selection in document. The selection string is generated for you automatically.
  4. Give the group a name, e.g., ChainA, and click Add index group to the list.

Add an index group for chain A

You can repeat this process to create a group for chain B. You can also test each group: select it from the list and click Select in document based on selection string. The corresponding atoms will be instantly highlighted in the Viewport, ensuring your selection is accurate.

Added index groups for chains A and B

What Makes This Useful?

This intuitive approach cuts down drastically on errors and iteration time. It’s especially beneficial for newcomers to GROMACS who may not be familiar with the intricacies of selection syntax. By removing the guesswork from index creation, SAMSON enables more confidence in system setup, which is crucial for complex workflows like umbrella sampling or steered MD.

Furthermore, it keeps everything context-aware. The generated groups are tied directly to the loaded structure, and selections remain visual and editable at any point during your workflow. It’s molecular modeling, made just a bit more relaxed.

For more details on this step and a full COM pulling tutorial, visit the original documentation: GROMACS Wizard – COM Pulling.

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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