When preparing molecular dynamics simulations with GROMACS, defining the right index groups can make a huge difference. These groups are essential for tasks such as computing interaction energies, defining pull coordinates, or applying restraints. However, creating these groups manually using gmx make_ndx can be time-consuming and error-prone—especially when dealing with complex systems or selection syntax.
Fortunately, if you use the GROMACS Wizard in SAMSON, you can define custom index groups through a visual, user-friendly interface that saves both time and effort.
What Are Index Groups and Why Do They Matter?
In GROMACS, index groups are arbitrary groups of atoms that you can define for analysis or simulation setup purposes. While GROMACS automatically generates standard groups (like Protein, SOL, Ions), researchers often need more specific selections—like residues in alpha helices, or all atoms near a particular ligand.
Traditionally, you’d specify these using the make_ndx tool and manually input atom ranges or selection commands. This can be quite a hurdle if you’re not fluent in GROMACS syntax, or if your system is large and complex.
Creating Custom Index Groups in SAMSON
The GROMACS Wizard in SAMSON makes it simple. Here’s how it works:
- Click on the Add/edit index groups button in the Prepare step of the GROMACS Wizard.
- This opens a pop-up window where you can manually enter a GROMACS selection string—or generate one automatically from your current selection in SAMSON.
- Use SAMSON’s visual selection tools to select atoms, residues, or chains. For example, go to
Select > Residues > Amino acids > Secondary structure > Alpha helices. - Then click Generate based on current selection in document. This auto-generates the GROMACS selection syntax.
- Name your group (e.g.,
HELICES) and click Add index group to the list.
The group is then saved in the index.ndx file in your project folder, ready to be used in the next steps of your simulation setup.
When and Why to Use This
Custom index groups are especially useful if you plan to run:
- Umbrella sampling: define pull groups and reaction coordinates
- Energy analysis: isolate specific residue or ligand contributions
- Protein-ligand simulations: apply restraints to defined fragments
This method also keeps your workflow reproducible—SAMSON stores these groups in your project, ready for reference or reuse.
Considerations
Before creating custom index groups, make sure your system has unique and consecutive indices for atoms and residues. Also note that you can add or modify index groups not only during the preparation phase, but also in minimization, equilibration, and production simulation stages.
To learn more and explore the full preparation workflow, including index groups, visit the official documentation page: GROMACS Wizard – Preparation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.