Easier Group Selection During MD: Creating Custom GROMACS Index Groups in SAMSON

Molecular dynamics (MD) simulations often require targeted control or analysis of specific parts of a structure—for example, calculating forces on side chains, analyzing water clusters, or applying constraints to ligand atoms. GROMACS automatically generates standard atom groups (like Protein, Water, or Ion), but these might not always meet a researcher’s needs.

For those needing custom index groups, SAMSON’s GROMACS Wizard simplifies this often tedious process. Instead of editing raw index files or running gmx make_ndx manually, SAMSON offers an interactive, visual method for defining and testing index groups using its built-in selection tools or GROMACS syntax.

💡 Why This Matters

Index groups are key for:

  • Defining pull groups in umbrella sampling or steered MD
  • Specifying temperature or pressure coupling groups
  • Custom analysis (e.g., RMSD of loop regions, distances between atom sets)

Doing this by hand is error-prone and slows down workflows. SAMSON makes it visual and fast.

Adding Custom Index Groups in SAMSON

You can add index groups at multiple stages: preparation, equilibration, and simulation. It’s most useful to edit or add them after preparation (during equilibration or simulation), when default groups are already loaded by GROMACS. This ensures you build on existing groups.

Step-by-Step Guide

  1. Load the system in SAMSON using the Load button next to the input path if it isn’t already open.
  2. Click the Edit index groups button.
  3. You will see the existing GROMACS groups listed. These are read-only but can be referenced when building new groups.
  4. You now have two paths:

    • Use the GROMACS syntax: For example "Protein" & ! "C-alpha" selects all protein atoms except C-alpha atoms.
    • Or, use SAMSON’s selection interface: Visually select atoms, then generate the selection string automatically.

Add a custom index group

Once selected:

  • Click + to start a new group
  • Click Generate based on current selection in document
  • Name your group and click Add index group to the list
  • Finally, click Apply to save the index group (it’s stored in index.ndx)

Example: Neutral Side Chains

Let’s say you want to create a group made up of side chain atoms from neutral amino acids. Instead of identifying residue IDs manually and writing out atomic selections, SAMSON allows you to visually select these based on residue properties:

  • Use Select > Residues > Amino acids > Side chain charge > Neutral
  • Click Generate based on current selection
  • Done! The wizard takes care of the GROMACS syntax

Select amino acid residues with neutral side chains

Create a custom index group

Final Thoughts

This feature saves time, reduces input errors, and allows a more exploratory and visual way of setting up simulations. Rather than struggling with lengthy selection commands or editing NDX files manually, you can trust SAMSON to streamline your workflow.

Learn more in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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