When setting up molecular simulations, especially with GROMACS, getting the selection of atom groups right is essential for accurate results and efficient analysis. This is where custom index groups come into play — a feature that can save you time and add precision to your simulation workflow.
If you’re using SAMSON’s GROMACS Wizard, you already benefit from automated generation of standard index groups (e.g., protein, solvent, ions). But sometimes, you need more: a specific domain of a protein, a ligand-binding pocket, or residues in alpha helices. That’s where custom index groups shine.
What are custom index groups?
Custom index groups are user-defined sets of atoms or residues that are used during GROMACS simulations. They’re especially useful for tasks like:
- Pulling simulations (e.g., umbrella sampling and steered MD)
- Monitoring specific properties like distances or angles
- Defining restraints or biasing groups
- Controlling thermostats or barostats on specific regions
Creating custom index groups in SAMSON
The GROMACS Wizard in SAMSON makes it straightforward to define these custom groups. You don’t have to manually write selection strings unless you want to — SAMSON can generate them automatically based on your visual selections.
Step-by-step:
- Click the Add/edit index groups button.
- In the popup window, select atoms or residues using SAMSON’s selection interface (e.g., select residues in alpha helices).
- Click Generate based on current selection.
- Name your group (e.g.,
HELICES). - Click Add index group to the list.
This process creates a new entry in your index.ndx file using the gmx make_ndx command. These groups can then be reused in subsequent steps, including energy minimization, equilibration, and production MD.
When to use custom index groups
If you find yourself repeatedly setting up similar simulations that require targeting the same parts of the system — for restraints, pulling, or measurement — using named index groups saves time and reduces guesswork.
It’s also a handy feature when analyzing trajectories post-simulation. You can directly refer to these groups in analysis tools like gmx distance or gmx energy instead of repeatedly specifying atom numbers or redefining selections.
Tips
- Remember that index groups rely on consistent residue and atom indexing — make sure your input files are clean and well-ordered.
- You can come back and add new custom index groups even in later steps of the workflow (e.g., during equilibration or simulation setup).
- Use descriptive names to keep things organized, especially if working on collaborative projects.
Here’s what your new group might look like in SAMSON’s document view after preparation:
For many users, the ability to define and reuse specific regions of interest in a flexible, visual way is a game changer for the GROMACS simulation workflow.
To learn more, visit the full documentation page on GROMACS Wizard Preparation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.