Avoid Repeating Yourself: Add GROMACS Index Groups Once for All Your Simulations

Defining custom index groups in GROMACS is a common need when preparing molecular dynamics simulations — whether to define pulling groups, track specific residues, or refine your analysis. But if you’re working with batch projects or running similar simulations across many systems, repeating this task over and over can quickly become a burden.

In this post, we’ll look at a practical solution using the GROMACS Wizard in SAMSON: how to define your custom index groups during the preparation step so they are reused automatically in every step and every subproject. This approach can save time and reduce errors — but it comes with a trade-off you should know about. Let’s dive in.

Why define index groups early?

When you’re running simulations on a single system, you can define custom index groups at the preparation, equilibration, or simulation step of the GROMACS Wizard. But when you’re using a batch project — for example, simulating multiple compounds or variants — the best strategy is to define the groups just once during the preparation step.

This way, the required groups (e.g., for pulling or restraints) will be automatically included in the index.ndx files of all subprojects, without having to redefine them individually. This can be a major time saver in large-scale studies or workflows.

📌 How are these groups stored? They’re saved in the project’s index.ndx file using the gmx make_ndx command, so they’ll be reused in all future steps, including equilibration and production runs.

What’s the catch?

There’s one limitation to be aware of: when creating index groups at the preparation step, GROMACS hasn’t yet generated its default groups (like Protein, Water, etc.). This means your selection strings can’t refer to those predefined groups since they don’t exist yet.

Also, in certain edge cases — particularly if your system has non-unique or non-consecutive atom or residue indices — indexing issues may arise. That’s why it’s recommended to check your output and verify that your new groups were created as intended.

When it’s a good fit

Use the preparation-step workflow when:

• You’re working with a batch project involving many systems.
• Your selection doesn’t require reference to GROMACS default index groups.
• You want consistent, reproducible groups across all runs.

How to do it in SAMSON

To create custom groups during preparation in the GROMACS Wizard:

1. Select the atoms or residues in the SAMSON interface. You can use the built-in selection tools (e.g., filtering by charge, type, or name).
2. Click the Edit index groups button.
3. Click + to start a new group, and then Generate based on current selection in document.
4. Name your group appropriately — this name will appear in your GROMACS selection strings.
5. Click Apply to save your custom group to the project’s index.ndx file.

Summary

Defining your custom index groups during the preparation step in SAMSON’s GROMACS Wizard can streamline the setup of large simulation projects by automating repetitive steps. Just make sure that your selection strings don’t depend on default GROMACS groups and test your selections when things look unusual.

Learn more in the full documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.