Effortlessly Define Custom Index Groups for GROMACS Simulations in SAMSON

When preparing molecular dynamics simulations using GROMACS, a common hurdle arises: how to define specific groups of atoms or residues for analysis, restraints, or pulling simulations. GROMACS provides a set of default index groups (such as Protein, Water, or Ions), but what if you need to isolate a specific chain or domain?

In SAMSON’s GROMACS Wizard, you can quickly create custom index groups directly from your molecular model—visually and intuitively—without having to dive into command-line tools or generate manual index files from scratch. If you’re struggling with complex selections in GROMACS, this could save you hours.

🧬 Why Custom Index Groups Matter

Index groups define which parts of your system you want to apply forces to, restrain, or monitor during simulations. For example, if you’re running a pulling simulation like COM (Center of Mass) pulling, you often need to specify two distinct chains: one to stay in place, and one to pull from.

While GROMACS generates automatic groups, most real-world systems are more nuanced—they might have multiple chains, ligands, or non-standard cofactors. Custom groups give you precise control over your system’s behavior.

📌 Step-by-Step: Adding Index Groups with SAMSON

Suppose you’re working with the 2BEG structure, which includes five chains. Imagine you want to run a COM pulling simulation where you pull Chain A from Chain B. Here’s how to set up Chain A and Chain B as custom index groups inside SAMSON’s GROMACS Wizard:

  1. Load the system: Use the Fetch tool in SAMSON to open the 2BEG structure.
  2. Open the Index Groups editor: In the Simulate tab of the GROMACS Wizard, click Edit index groups.

Edit index groups

  1. Select Chain A in the Document View.
  2. In the Index Groups window, click Generate based on current selection in document. This will auto-generate a selection string.
  3. Name your group ChainA and click Add index group to the list.

Add index group for Chain A

  1. Repeat steps 3–5 for Chain B, naming the group ChainB.

Add index group for Chain B

Once completed, you’ll see both custom groups listed and ready to be used for pulling simulations, restraints, or analysis.

Index groups for chains A and B

🎯 Practical Benefits

Using this graphical workflow in SAMSON makes it easy to:

  • Visually confirm your selected molecules
  • Avoid mistakes in selection definitions
  • Quickly create multiple index groups
  • Tie selections directly to GROMACS simulations downstream

It’s a simple but powerful step that streamlines simulation setup and minimizes debugging time later on.

To learn more about setting up pulling simulations and other workflows, visit the full tutorial page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.

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