When working with biomolecular simulations, especially in large and complex systems, index groups are essential. They define subsets of atoms in your system and can be used during simulation setup, analysis, or when applying constraints or forces. GROMACS automatically creates default groups based on system structure, but what if you need to target a specific set of atoms—like all neutral side chains or custom regions in a protein? This is where custom index groups become essential.
In SAMSON’s GROMACS Wizard, creating your own index groups is not only possible—it’s intuitive. Whether you’re analyzing the pull force on a specific domain or filtering data from a subset of residues, the flexibility to define your custom index groups can save time and increase precision.
Why Custom Groups Matter
By default, GROMACS includes groups like Protein, Water, or Ion. But for sophisticated simulations and downstream analysis, you may want to define specific atom selections—for instance, all non-C-alpha protein atoms or residues with neutral side chains.
For example, if you are interested in tracking the behavior of side chains with specific charges or isolating flexible loops in a protein, a custom group can help focus your pulls, restraints, or RMSD calculations.
Adding Custom Index Groups in Practice
To create custom index groups during the equilibration or simulation steps in GROMACS Wizard, first make sure your simulation system is loaded in SAMSON. If it’s not, simply click the Load button near the input path.
Then follow these steps:
- Click the Edit index groups button to open the GROMACS Index Groups window.
- Here you’ll see existing, default index groups. These can’t be edited, but they can be used as building blocks for defining new groups.
There are two main paths to create custom index groups:
- Using GROMACS selection syntax directly: Build logical selection strings using operations like
&(AND),|(OR), and!(NOT). For example,"protein" & ! "C-alpha"selects all non-C-alpha atoms in the protein. - Using SAMSON’s selection interface: Visually select atoms or residues in the 3D interface, and let GROMACS Wizard generate the index group syntax automatically.
For instance, if you select all residues with neutral side chains from the menu Select > Residues > Amino acids > Side chain charge > Neutral:
Then simply click + in the GROMACS Index Groups window and click Generate based on current selection in document. SAMSON will generate the appropriate GROMACS selection string, name your group, and allow you to add it to the project.
Click Add index group to the list and then click Apply to save it. Your new group is written to the index.ndx file in the project directory, ready to be used in subsequent steps.
One Tip to Remember
If your system has non-consecutive or non-unique atom/residue indices, adding index groups too early (e.g., during the preparation step) may cause inconsistencies. For batch systems, however, it’s preferred to add them early to maintain consistency across sub-projects.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net