Creating Custom Index Groups for GROMACS Pulling Simulations in SAMSON

When performing molecular dynamics simulations with GROMACS, creating custom index groups is often a source of friction—especially for those performing pulling simulations. Manually generating index files (.ndx) using the GROMACS command line can be tedious and error-prone, particularly for users unfamiliar with GROMACS scripting. Fortunately, the GROMACS Wizard Extension in SAMSON streamlines the process by offering a graphical interface for defining and managing custom index groups.

Let’s explore a typical use case: you’re simulating the center-of-mass (COM) pulling of a protein complex and need to define two chains—say, chains A and B—as reference and pull groups. Instead of using make_ndx in the terminal, SAMSON allows you to do everything visually.

Defining Index Groups in SAMSON

Suppose you’ve already loaded PDB ID 2BEG into SAMSON. This structure includes multiple chains. To define chains A and B as separate index groups:

  1. Select chain A in the Document view.
  2. Open the Index Groups window by clicking on Edit index groups within the Simulate tab of the GROMACS Wizard.
  3. Click Generate based on current selection in document – SAMSON populates the selection string automatically.
  4. Name the group (e.g., ChainA) and click Add index group to the list.

Add an index group for chain A

Repeat this process for chain B to create the second group.

Add an index group for chain B

Once both index groups have been added, they appear in the custom group list and can be selected directly in the simulation setup.

Added index groups for chains A and B

Why This Matters

Defining precise atomic groups is essential for pulling simulations, umbrella sampling, or restraint-based operations in GROMACS. Errors or ambiguity in group definition can lead to faulty simulations or unexpected forces. By managing these groups visually and interactively in SAMSON, you:

  • Save time by avoiding terminal-based input files.
  • Reduce risk of syntax errors in group definitions.
  • Instantly verify selections using visual feedback.

Additionally, SAMSON allows users to click on a custom group and Select in document based on selection string—a helpful verification step to ensure accuracy before launching the simulation.

Select nodes from an index group

This approach makes defining groups for COM pulling—such as pulling chain A from chain B—much more accessible, even for newcomers to molecular dynamics.

To learn how this integrates into a full pulling simulation workflow, visit the full documentation page: 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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