When setting up a simulation involving custom pulling forces in GROMACS, one of the first roadblocks many molecular modelers face is the creation of appropriate index groups. These groups are essential to define regions of interest in biomolecular simulations—whether you’re pulling a domain, fixing a part of a protein, or applying restraints.
Traditionally, defining these groups requires working with GROMACS’ make_ndx command-line utility and selecting atoms based on numerical IDs or name patterns. This process, while powerful, is error-prone and time-consuming for visual tasks like selecting specific chains.
This blog post explains how you can use SAMSON’s GROMACS Wizard to define custom index groups visually, directly from your molecular models—in a much simpler and intuitive way. Whether you’re performing center-of-mass (COM) pulling or umbrella sampling, this step is crucial to set up your system correctly.
Visual Selection of Chains in SAMSON
Let’s say you are preparing a COM pulling simulation on the 2BEG system. You want to:
- Pull Chain A
- Restrain Chain B
To do that, you need to define Chain A and Chain B as separate index groups.
Using SAMSON:
- First load the system in SAMSON via the GROMACS Wizard.
- Open the “Edit index groups” window in the Simulate tab of the wizard.
- Select the molecular fragment you need—e.g., Chain A—in the document.
- Click “Generate based on current selection in document”.
- Name the group (e.g.,
ChainA) and click “Add index group to the list”.
Repeat this process for Chain B. You now have two crystal-clear groups defined precisely as you see them in the 3D view. No need to guess atom indices or manually navigate GROMACS terminal-based selection tools.
Preview and Verify
One handy trick is that you can visually verify your index groups. Once your group is created, just select it from the list and hit “Select in document based on selection string”. You’ll immediately see the selected nodes light up, so you can be sure everything is defined correctly—saving time and avoiding mistakes further down the pipeline.
Why It Matters
Correctly defining index groups isn’t just a best practice—it’s absolutely necessary when applying forces in production molecular dynamics simulations. Inaccurate group definitions can lead to meaningless results—or worse, unstable simulations. Being able to do this visually means:
- Faster setup
- Reduced errors
- Improved reproducibility
With SAMSON and the GROMACS Wizard, this workflow becomes far more approachable, especially for those who prefer visual tools over command-line scripting.
Learn More
If you’re preparing simulations involving COM pulling, check out the full tutorial at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.