When working with molecular simulations in GROMACS, fine-tuning your index groups can unlock more targeted analysis, steering, and restraint strategies. However, knowing when to add these custom groups can make a big difference—especially if you want to avoid errors and repeat steps in your simulation workflow.
This post explores the often-overlooked pitfall of indexing errors when adding custom index groups during the preparation step in SAMSON’s GROMACS Wizard. We’ll explain what causes these errors, and how to avoid them based on your project setup.
Why Add Custom Index Groups?
Index groups in GROMACS define subsets of atoms, and are critical for tasks like applying restraints, defining pull groups in umbrella sampling, or extracting meaningful trajectories. While GROMACS generates standard index groups automatically (like ‘Protein’, ‘Water’, etc.), custom groups allow a more tailored approach—for instance, selecting only neutral side chains, or atoms in a specific loop region.
The Preparation Step Dilemma
In principle, you can add custom index groups during any simulation stage: preparation, equilibration, or production. But SAMSON allows this already at the preparation step, which is convenient—especially if you’re working with batch simulations spanning many subprojects.
However, there’s a subtle challenge: default index groups from GROMACS are not yet generated at the preparation step. This means you can’t define new groups based on those defaults (such as combining “Protein” with “! C-alpha”, for instance), because they don’t exist yet at that point in the workflow.
Common Indexing Errors and How to Prevent Them
When working at the preparation step, if your structure contains non-unique or non-consecutively numbered atoms or residues (common when modifying PDBs manually or merging structures), GROMACS might not interpret selection strings correctly. This can result in broken groups and simulation errors later on.
Warning
When adding index groups at the preparation step, if your system has non-unique or non-consecutive indices for residues and atoms then in some cases there might be issues in indexing. So, it is better to verify afterward that the groups were generated as you wanted them, or, for a single project, to add these groups e.g. at the equilibration or simulation steps.
What We Recommend
- If you’re processing many similar systems in a batch: Define your custom groups in the preparation step, and verify them thoroughly before proceeding to equilibration.
- If you’re working on a single project or if your system has complex or manually-edited topology: Add custom groups after the preparation step, during equilibration or simulation. By then, GROMACS has already generated default index groups, reducing the chances of mismatches.
In short, while early selection saves time for batch jobs, later selection often saves the day for uniquely-structured projects.
To learn more and see detailed examples with screenshots, visit the full documentation at:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/adding-custom-index-groups/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.