When setting up molecular simulations, one common pain point for many researchers is the need for finer control over atom groups used in analysis or simulation inputs. While GROMACS provides standard index groups like protein, water, or ions by default, scenarios often arise where you need more specific selections based on your research goals — for example, selecting only neutral side chains or excluding backbone atoms.
Fortunately, the SAMSON GROMACS Wizard makes it easier to define custom index groups at different stages of your simulation workflow. In this post, we’ll explore how to create and manage these groups during the equilibration and simulation steps — a practical and flexible option when the default GROMACS groups are already available.
Why Add Custom Index Groups?
Let’s say you’re planning to use pull groups for umbrella sampling or want to track a specific side chain interaction. Custom groups help you specify these atom sets precisely without manual edits to index files. They also improve clarity when analyzing trajectories, calculating distances, or applying constraints.
Step-by-Step: Adding Custom Groups in Equilibration/Simulation Steps
1. Load Your System
If the project isn’t already open, click the Load button next to the input path in the SAMSON GROMACS Wizard.
2. Access Index Group Management
Click on Edit index groups to open the dedicated interface.
3. Review Existing Index Groups
You’ll see the default index groups generated by GROMACS. These are useful references but cannot be changed. However, you can use them in your selection syntax for building new groups. Click Select in document based on selection string to visualize any of them.
Two Approaches for Custom Selections
Option 1: Using GROMACS Selection Syntax
You can enter logical expressions based on existing group names. For example:
"protein" & ! "C-alpha"
This selects all protein atoms except for the C-alpha atoms. Click Test selection string to check if it selects what you expect.
Option 2: Using SAMSON’s Visual Selection
If you prefer a visual interface, SAMSON allows selective highlighting. For example, choose:
Select > Residues > Amino acids > Side chain charge > Neutral
Then, return to the GROMACS Index Groups window, click + to begin a new group, and choose Generate based on current selection in document. SAMSON will automatically generate the appropriate GROMACS selection string based on your selection.
Finally, name the group, click Add index group to the list, and then Apply. This custom group will be saved in the index.ndx file inside your project directory.
Why Add Groups at This Stage?
Adding custom groups during equilibration or simulation gives you access to all the default groups generated during preparation, offering more flexibility. You can also verify the correct selection of atoms before proceeding to time-consuming simulations.
This feature streamlines setup for advanced simulation protocols and makes batch simulations with consistent group definitions easier to manage.
Want to explore more details or re-read some step-by-step instructions? Visit the full documentation page on Adding Custom Index Groups with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.