Creating Custom Index Groups for Center of Mass Pulling in GROMACS Wizard

Defining custom index groups can often be one of the trickiest steps for molecular modellers when setting up pulling simulations in GROMACS. If you’re performing center-of-mass (COM) pulling, it’s crucial that the pulled and reference groups are properly defined. In this blog post, we’ll focus on how SAMSON’s GROMACS Wizard streamlines the process of creating these groups—without the need to manually edit cumbersome index files 🎯.

Why custom index groups matter

By default, GROMACS provides a standard set of index groups (e.g., Protein, Water, Ions). But in pulling or umbrella sampling simulations, you usually want to define more specific regions of your system—such as a particular chain or protein domain—as the source and target of the pulling force. Without this, your simulation might not pull the atoms you intended, or might not run at all. 👀

How it works in SAMSON

Once you’ve equilibrated your system, head to the Simulate tab in the GROMACS Wizard. There, under the COM pulling section, click Edit index groups.

Edit index groups

Step-by-Step: Creating Custom Groups

Let’s say you want to pull Chain A relative to Chain B in a complex protein structure—like in the 2BEG system used in this tutorial. Here’s how to do it:

  1. Load your prepared system in SAMSON by clicking Load in the Input section.
  2. In the Document view, select Chain A.
  3. In the Index Groups window, click Generate based on current selection in document.
  4. Name the group ChainA and click Add index group to the list.

Add an index group for chain A

  1. Repeat the same steps for Chain B and name it ChainB.

Add an index group for chain B

Once defined, you can verify your groups by selecting them from the list and clicking Select in document based on selection string. It’s a great way to avoid mistakes, especially with large molecular systems.

Select nodes from an index group

Why this matters

In traditional workflows, generating index groups usually requires going through an interactive terminal session with make_ndx. This adds a manual step, error-prone formatting, and can be time-consuming. SAMSON’s graphical interface streamlines this step while making it easier to verify that you’ve selected the correct atoms. Especially for beginners or for simulations involving many chains or residues, this saves time and reduces mistakes.

What’s next?

Once your groups are defined, you can jump straight into specifying your pulling parameters. Define the pulling type, geometry, and rate directly in the wizard. No need for manual .mdp file editing.

To learn more, visit the full tutorial page on 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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