A Practical Guide to Setting Up Custom Index Groups for Pulling Simulations in GROMACS Wizard

Setting up center-of-mass pulling simulations in GROMACS often requires the definition of custom index groups—particularly when dealing with multi-chain protein systems. For many molecular modelers, this step introduces friction, especially if you’re switching between the command line and visualization tools.

Fortunately, if you’re using the GROMACS Wizard in SAMSON, defining custom index groups is much more intuitive and interactive. This blog post walks you through how to efficiently prepare index groups for pulling chain A away from chain B using GROMACS Wizard.

Why Custom Index Groups Matter

When configuring pulling simulations, it’s crucial to identify exactly which atoms or chains to apply the pulling force to (pull group), and which to use as reference (reference group). GROMACS default groups like ‘Protein’ or ‘Water’ aren’t always enough—you often need to create specific selections, such as individual chains.

Visual Group Creation in SAMSON

Unlike manually editing index files or working through command-line prompts, SAMSON allows interactive group definition within the molecular viewer. Here’s how:

  1. First, finish your system setup and jump to the Simulate tab in GROMACS Wizard (COM Pulling step).
  2. Click Edit index groups to access the full list of currently available groups.

Edit index groups

Adding Chain A as a Group

  1. In the Document view, select chain A.
  2. Return to the Index Groups window and click Generate based on current selection in document.
  3. Name the group ChainA and click Add index group to the list.

Add index group for chain A

Repeat for Chain B

  1. Select chain B in the Document view.
  2. Repeat the action in the Index Groups window. Name it ChainB.

Add index group for chain B

Double-Check Selections

Now that you’ve added the custom index groups, you can verify them conveniently:

  • Select a group from the list
  • Click Select in document based on selection string to highlight it in the molecular viewer

Test index group selection

Use in COM Pulling Parameterization

With the index groups ready, you can define precise pulling parameters where, for example, ChainA is pulled from ChainB in the z-direction. This step ensures your simulations are setup accurately and reproducibly.

Pro tip: Group creation is only available if you’ve imported the prepared structure. Use the Load button in the Input section to do so.

From a practical standpoint, this group-defining interface combined with SAMSON’s visualization saves time and reduces errors—especially for users new to GROMACS or those working with complex systems.

To learn more about center-of-mass pulling setups and subsequent steps, visit the full documentation page here: 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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