Anyone who’s worked with GROMACS knows how essential index groups are when setting up complex molecular dynamics simulations. Whether you’re pulling a specific domain during umbrella sampling or analyzing RMSD for specific atoms, you typically need to create custom index groups. But if you’re not a fan of editing index.ndx files manually — or struggling with command-line syntax — GROMACS Wizard in SAMSON offers a graphical, streamlined alternative.
Custom index group creation often becomes a tedious bottleneck:
- You have to ensure residues and atoms are correctly indexed.
- You need to master the
gmx make_ndxsyntax. - Maintaining consistency in group definitions across simulations isn’t always trivial.
SAMSON’s GROMACS Wizard simplifies this with a visual, integrated interface that lets you select atoms or residues directly in 3D and generate GROMACS-compatible index groups with a click. Here’s how it solves the problem:
Visual Selections → Index Groups
Instead of writing selection syntax manually, you can use SAMSON’s extensive selection mechanisms—like selecting protein secondary structures from a graphical menu. For example, select all alpha helices via:
Once you’ve made your selection, click "Add/edit index groups" and then "Generate based on current selection in document".
The GROMACS selection string is created automatically. All you need to do is name the group (e.g., HELICES) and click Add index group to the list:
Why this matters for real workflows
By visually selecting atoms, you significantly reduce human error—no more typing wrong residue numbers or misnaming atoms. This is particularly useful if you’re dealing with:
- NMR structures with multiple conformations
- Proteins with large loops/topics you want to manipulate
- Simulations involving non-standard residues or ligands
The index groups you add are saved in the index.ndx file in your project folder and can be reused in future steps: minimization, equilibration, simulation, or analysis.
And don’t worry — if you forgot something, you can always edit or add index groups in the next simulation steps.
Before You Begin
- Make sure your system has unique and consecutive atom and residue indices.
- No need to install scripts or command-line tools separately — everything is integrated within GROMACS Wizard in SAMSON.
If your simulation needs precise control at the atom or residue level, GROMACS Wizard offers an intuitive, GUI-based solution that side-steps the traditional headaches of custom index group generation. This is a real time-saver for anyone who runs advanced simulations, especially involving collective variables or multistep workflows.
Learn more about this feature and others in the full documentation at GROMACS Wizard – Prepare.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.