Creating Custom Index Groups for Targeted COM Pulling in GROMACS

In molecular dynamics setups using GROMACS, defining appropriate index groups is essential when applying center-of-mass (COM) pulling between specific parts of a molecular system. However, this can be a challenge, especially when your regions of interest aren’t part of GROMACS’ default index groups like Protein, Water, or Ions.

Let’s say you are doing a pulling simulation on the 2BEG protein structure, where chains A and B represent the interaction of interest. If you need to pull chain A away from chain B, you first need to define these regions as custom index groups. SAMSON’s GROMACS Wizard makes this process more intuitive with visual support. Here’s how you can go from confusion to a ready-to-run simulation in just a few clicks.

Why It Matters

When COM pulling between two chains or domains, GROMACS requires that you define them as atom index groups. If these groups don’t exist in the base set, your simulations may either fail or result in unintended behavior. Creating precise index groups ensures control over which atoms are being pulled and which serve as reference points.

Step-by-Step: Adding Chain-Based Index Groups

Let’s walk through the process of creating index groups for chain A and chain B directly in SAMSON:

  1. First, load the structure in SAMSON (e.g., 2BEG).
  2. In the Document View, select chain A.
  3. Click Edit index groups in the GROMACS Wizard interface.

Edit index groups

  1. Click Generate based on current selection in document – this populates a selection string automatically.
  2. Set the name of the group to ChainA.
  3. Click Add index group to the list.

Add an index group for chain A

Now repeat the process for chain B:

  • Select chain B from the Document view.
  • Generate the selection string, name the group ChainB, and add it.

Add an index group for chain B

Check Your Work

You can validate each index group by selecting it from the list and clicking Select in document based on selection string. This highlights the atoms in the 3D viewport directly, helping you confirm that everything is selected correctly before proceeding with the simulation.

Select nodes from an index group

When to Use Custom Index Groups

This feature becomes particularly useful when your simulation involves pulling, restraints, or region-based analysis that involves non-standard selections (specific chains, residues, or atoms). Instead of crafting complex index files manually, you can generate and test groups visually within SAMSON.

What’s Next?

After defining your custom groups, you can move on to configure pulling parameters under the COM Pulling section of the Production MD tab. Using your new ChainA and ChainB groups, you can specify the pulling geometry, direction, and rate with confidence that you’re targeting exactly the atoms you expect.

Learn more about this feature and how it fits into the full pulling simulation tutorial 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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