Quickly Creating Custom Index Groups in GROMACS with SAMSON

When setting up molecular dynamics simulations with GROMACS, a recurring pain point for researchers is managing index groups. These groups—collections of atoms used to define restraints, pulling, or analysis regions—often need to be manually created through command line inputs in GROMACS. This can become cumbersome, especially for complex biomolecular systems where precision matters.

In the GROMACS Wizard within SAMSON, this process becomes significantly faster and more visual. Here’s how to use SAMSON to generate custom index groups quickly, without worrying about syntax errors or manual group numbering.

Why Custom Index Groups Matter

Index groups allow you to:

  • Apply restraints or forces to specific parts of your system
  • Define regions for pulling or umbrella sampling
  • Streamline selection for analysis in post-processing

By default, GROMACS assigns basic groups like Protein, Water, and Ions. But what if you just want to pull chain A with respect to chain B? That’s when custom groups are necessary.

Creating Index Groups in SAMSON

Once your system is loaded in SAMSON (e.g., the 2BEG protein complex), follow these steps:

  1. Switch to the Simulate tab in the GROMACS Wizard.
  2. Click the Edit index groups button.
  3. In the new window, select the part of the system you want to include in your new group, for example, chain A.
  4. Click Generate based on current selection in document.
  5. Give your index group a name, such as ChainA.
  6. Click Add index group to the list.

Repeat this process for chain B, or any subset you need. Selections are made visually in the Document view, which helps reduce errors that are easy to make with atom index lists or selection strings from scratch.

Add an index group for chain A

Add an index group for chain B

Verifying and Testing

You can double-check your new groups easily:

  1. Select a group from the list.
  2. Click Select in document based on selection string.

This instantly highlights the selected group in your loaded structure, letting you confirm your choice without running a trial simulation.

Added index groups for chains A and B

What This Solves

Instead of typing atom numbers manually or scripting the creation of index groups, SAMSON users can rely on this GUI-based workflow that integrates visual feedback and intuitive controls. This is particularly useful for workflows involving chain-specific manipulations—such as pulling, restraining, or tracking dynamic properties over time—often needed when preparing umbrella sampling or steered MD simulations.

If you’ve been toggling between visualization tools and text-based index editing, this approach can reduce the chances of mismatch errors and accelerate your setup process.

Learn more about the full COM pulling workflow, including system preparation, energy minimization, NPT equilibration, and simulation setup, in the full tutorial.

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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