Molecular dynamics simulations often require finer control over system components for applying specific actions like restraints, pulling, or analysis. In GROMACS, this is handled through index groups. While GROMACS automatically creates standard groups (like protein, water, ions), there are many situations where adding custom index groups is crucial—for instance, isolating a ligand binding site, neutral residues, or any subset relevant to your study.
If you’re using SAMSON’s GROMACS Wizard, you might be wondering: What’s the best moment to add these custom index groups?
What’s the difference between preparation, equilibration, and simulation steps?
In a typical GROMACS workflow—whether for a single system or a batch of systems—you’ll go through three major phases: preparation, equilibration, and simulation. Each of these phases affects how and when you should add custom index groups. Let’s break this down.
Adding Index Groups at the Preparation Step: Pros & Cons
Adding custom groups early, at the preparation step, is efficient when you’re working with batch projects. That’s because you define the groups once, and they get propagated to all subprojects. But there’s a catch: at this stage, default index groups haven’t been generated by GROMACS yet, so you can’t use them in your selection strings.
Warning
If your molecular system contains residues or atoms that don’t have unique consecutive indices, custom groups might not be generated correctly. It’s a good idea to verify afterward or defer group creation until later stages.
Why the Equilibration or Simulation Steps Might Be Better
At the equilibration and simulation stages, you’ll already have access to GROMACS’s default index groups, making it easier to write selection expressions using existing group names.
This means you can create more flexible selections, like selecting non-C-alpha atoms using an expression such as:
|
1 |
"protein" & ! "C-alpha" |
This type of logic gives better control and avoids errors due to incomplete system data.
Interactive Editing with the GROMACS Wizard Interface
Adding groups during equilibration or simulation is also more interactive. You can:
- Click Edit index groups to view existing index groups.
- Use preset selection tools in SAMSON to highlight parts of the system.
- Click Generate based on current selection to auto-generate the GROMACS selection string.
- Name the group and click Add index group to the list.
This is especially useful for selections that aren’t trivial to express in GROMACS language—like residues with neutral side chains, or excluding water and ions automatically.
What’s the final takeaway?
If you’re working on a batch project, try defining your index groups during preparation—just be cautious about group accuracy. If you’re on a single project or want greater group flexibility, define your custom groups during the equilibration or simulation phase. This allows you to leverage default groups, test your selection in SAMSON, and catch potential mismatches early.
To explore the full tutorial on working with custom index groups in the GROMACS Wizard, visit the official documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/adding-custom-index-groups/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.