When setting up GROMACS simulations, many molecular modelers reach a point where they need to define custom index groups — for example, to monitor specific residues, apply restraints, or use them as pulling groups during simulations. While gmx make_ndx is the standard GROMACS tool for doing this, it can feel obtuse, especially when working with complex systems or when identifying atoms based on structural elements like secondary structure.
If you’re using the SAMSON GROMACS Wizard, there’s a streamlined and visual way to generate and include custom index groups directly into your workflow. This feature can save you time and help avoid manual errors when writing selection commands from scratch.
Why Use Custom Index Groups?
Custom index groups allow you to select specific sets of atoms or residues based on your research needs. Typical use cases include:
- Selecting specific parts of a molecule involved in binding or catalysis.
- Tracking atoms across frames to compute RMSDs or other observables.
- Specifying pull groups in enhanced sampling methods.
- Facilitating focused analysis post-simulation.
The challenge? Accurately constructing these selections — especially for systems with multiple models, inconsistent indexing, or complex structural properties.
How SAMSON Makes This Easier
SAMSON provides an intuitive interface for creating custom index groups using its flexible selection tools. You can use GROMACS syntax directly or rely on SAMSON’s graphical selection interface:
- Click on Add/edit index groups in the GROMACS Wizard.
- Use SAMSON’s selection menu (e.g., Select > Residues > Amino acids > Secondary structure > Alpha helices) to highlight the atoms you’re interested in.
- Click Generate based on current selection in document to automatically produce a GROMACS-compatible selection string.
- Give the group a name (e.g.,
HELICES), test the string if needed, and click Add index group to the list.
Here’s a breakdown of the interface at various stages:
Once added, the index group will be stored in the index.ndx file and listed in the prepared system document in SAMSON, ready to be used during minimization, equilibration, or production runs.
Things to Keep in Mind
- You can create and edit index groups later on during other simulation stages.
- Ensure that residue and atom indices in the system are unique and consecutive — this is essential for accurate group definitions.
- If you decide to work with coarse-grained models, refer to the specific documentation on compatibility with CG systems.
By using SAMSON’s integrated selection tools, you reduce the likelihood of misidentifying atoms based on raw indices or manual inspection, and make your simulation setup more intuitive and reproducible.
Learn more about custom index groups and the full preparation process on the GROMACS Wizard documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.