Creating Custom Index Groups for Precise Pulling Simulations

Molecular modelers often face a common hurdle when setting up pulling simulations using GROMACS: how to define custom index groups that don’t appear in the default list. Whether it’s pulling a specific protein chain or restraining a certain region of the molecule, having fine control over molecular groups is essential for accurate center-of-mass (COM) pulling simulations.

In the GROMACS Wizard Extension within SAMSON, customizing index groups is made visually intuitive. If you’re planning to simulate interactions such as pulling chain A away from chain B (as in the 2BEG system example), this guide will show you how to define the necessary index groups inside SAMSON’s graphical interface.

Why Defining Index Groups Matters

By default, GROMACS provides standard groups like Protein, Water, and Ions. But for specific tasks such as restraining a unique domain or applying custom forces to selected chains, users need to define their own index groups.

Without this step, you’re limited in your ability to target exact molecular substructures during simulations, which can lead to inaccuracies or reduced insight into specific molecular mechanisms.

How to Add Custom Index Groups for Pulling

Imagine you’re setting up a COM pulling simulation where chain A must be pulled away from chain B. Here’s a streamlined, visual walkthrough of how to define these custom groups in SAMSON:

1. Ensure the System is Loaded

Use the Load button in the Simulate tab to import your prepared structure into SAMSON. This step enables live selection for index generation.

2. Open the Index Groups Editor

Click Edit index groups to access the interface for viewing and creating custom groups:

Edit index groups

3. Select Chain A and Add as a Group

  • Select chain A from the Document view.
  • In the Index Groups window, click Generate based on current selection in document.
  • Name the group ChainA and click Add index group to the list.

Add chain A

4. Repeat for Chain B

  • Select chain B in the same way.
  • Generate the selection string and name the group ChainB.
  • Add it to the index group list.

Add chain B

Now you’ll see both groups listed and ready for use in your pulling configuration:

Custom index groups

Test Your Groups

You can validate your custom index groups by selecting one from the list and clicking Select in document based on selection string. This helps ensure that you’ve correctly defined each group before launching costly simulations.

Test select group

When to Use This

Any time your simulation requires force application or restraints on non-standard parts of the molecule (like individual chains, ligands, or domains), defining custom index groups becomes crucial. Especially in COM pulling or umbrella sampling setups, it ensures physical relevance and accurate mechanical control during simulations.

Being able to easily define these groups visually in SAMSON not only accelerates setup but also minimizes input errors that are common when manually editing index files.

Learn more about setting up simulations with GROMACS Wizard by visiting the full COM Pulling tutorial page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

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