Defining Custom Index Groups for COM Pulling in SAMSON

When setting up center-of-mass (COM) pulling simulations in GROMACS using SAMSON’s GROMACS Wizard, one key step that often raises questions is how to properly define and use custom index groups. This step is essential if you want to pull specific chains—or any molecular groups—not present in the default GROMACS index selections like Protein, Water, or Ions.

This brief guide will walk you through setting up your custom index groups to perform a COM pulling simulation where one chain is pulled away from another—precisely what many molecular modelers need for protein-ligand unbinding or protein-domain dissociation studies.

Why Custom Index Groups Matter

Default index groups work for many scenarios but fall short when you’re interested in specific fragments of your system, especially when performing targeted simulations like pulling chain A away from chain B. Defining proper groups ensures your pulling parameters are physically meaningful and that the simulation behaves as expected.

Preparing the Scene

Before defining your groups, make sure your system is loaded in SAMSON. You can use the Load button in the Simulate > Input section to bring your molecular structure into the workspace. This view will support intuitive atom and chain selection.

Step-by-Step: Creating Custom Index Groups

1. Open Index Group Editor

Click the Edit index groups button in the Simulate tab. A window will open showing predefined GROMACS groups and allowing you to add new ones.

Edit index groups

2. Create an Index Group for Chain A

  1. In the Document view, select chain A.
  2. In the Index Groups window, click Generate based on current selection in document. This auto-fills the selection string.
  3. Name the group e.g., ChainA.
  4. Click Add index group to the list.

Add index group for chain A

3. Repeat for Chain B

  1. Select chain B in the Document view.
  2. Click Generate based on current selection in document.
  3. Name the group ChainB.
  4. Click Add index group to the list.

Add index group for chain B

Validation: Check Your Selection

Once added, you can verify your group by selecting it from the list and clicking Select in document based on selection string. This highlights the atoms in the Viewport, ensuring your groups are correctly defined.

Test index group selection

Using Your Custom Groups for Pulling

Once defined, these groups (e.g., ChainA and ChainB) appear in the dropdowns of the COM pulling setup. You can now configure a pulling coordinate where one group moves relative to the other, with control over pulling direction, distance, and force constants.

This process allows you to run targeted molecular dynamics simulations with fine-grained control—ideal for probing intermolecular forces or generating data for umbrella sampling.

To learn more about how to configure the full pulling simulation—including energy minimization, NPT equilibration, and production MD—visit the official GROMACS Wizard – COM Pulling tutorial.

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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