Avoiding a Common Mistake in GROMACS: Custom Index Groups for COM Pulling

Setting up center-of-mass (COM) pulling simulations in GROMACS can be a highly rewarding approach to explore molecular interactions and conformational changes. But there’s a frequent stumbling block that frustrates even experienced molecular modelers: missing index groups.

When setting up a pulling simulation, you often need to define specific molecular regions as pull groups. For example, to pull one protein chain (say, chain A) away from another (chain B), GROMACS needs to know which atoms belong to those chains. Default index groups such as “Protein” or “Water” don’t always offer the granularity required — and this is exactly where custom index groups come in.

Fortunately, SAMSON’s GROMACS Wizard makes creating and managing these groups much easier than doing it manually via command line. Here’s how you can avoid this frequent pitfall and set up your own index groups visually and intuitively.

Why Custom Index Groups Matter

If the groups you want to pull are not part of GROMACS’s default index groups, your simulation will either fail or behave incorrectly. Users often overlook this until it’s too late — and then need to backtrack.

In the context of COM pulling, let’s say you want to:

  • Pull chain A (movable)
  • Keep chain B fixed (reference)

To do this, both chains must be clearly defined in the input as separate index groups — and this is not automatic. Fortunately, SAMSON helps automate the tedious work of writing index files manually.

Step-by-Step: Defining Index Groups in SAMSON

1. Load the structure in SAMSON and make sure the Document view is displaying each chain distinctly.
2. Select chain A in the structure tree.

3. Click Edit index groups in the GROMACS Wizard:

Edit index groups

4. Click Generate based on current selection in document. Then name it ChainA and click Add index group to the list:

Add an index group for chain A

5. Repeat the same for chain B, giving it the name ChainB:

Add an index group for chain B

6. You should now see both groups available:

Added index groups for chains A and B

Test Your Groups

Select a group and use the button Select in document based on selection string to visually verify your group includes the correct atoms:

Select nodes from an index group

Takeaway

This step might seem small, but failing to create accurate custom index groups can derail an otherwise flawless simulation. Whether you’re pulling chains apart, restraining substructures, or setting up umbrella sampling — defining your groups early and clearly avoids unnecessary frustration.

For more guidance on COM pulling simulations in SAMSON’s GROMACS Wizard, visit the full tutorial: GROMACS Wizard – COM Pulling.

Note: 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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