Molecular simulation workflows often demand flexibility, especially when it comes to tracking specific parts of a system. GROMACS users know how critical index groups are—they define atom selections used in restraints, pulling, or analysis. While GROMACS automatically generates common index groups (like Protein, Water, or Ion), researchers frequently need custom groups that reflect specific regions of interest.
Doing this manually outside of a GUI can be time-consuming and error-prone. Fortunately, SAMSON’s GROMACS Wizard simplifies this step, especially during the equilibration or simulation stages. This is particularly convenient because, by then, the default GROMACS index groups are already available, allowing users to build on top of them. Here’s how molecular modelers can benefit—and avoid common errors—when incorporating custom index groups during equilibration.
Why Add Custom Index Groups at Equilibration?
During the system preparation phase, index groups can be added, but there’s a catch: GROMACS hasn’t yet generated its standard groups. That means you can’t reference them—or build on them—which may limit your flexibility. At the equilibration stage, however, those groups are already in place. You can preview them, selectively include parts, exclude others, or combine them in meaningful ways.
Getting Started in SAMSON
To begin, ensure the system is loaded in SAMSON. If not, simply click the Load button next to the input path. Then, click Edit index groups to open the index group editor.
Default groups appear in the editor but can’t be modified. You can select any of them in your document to visually inspect them—helpful for verifying if a group includes the atoms you expected.
These groups are also referenced directly in the document folder, and double-clicking them selects the relevant atoms:
Two Ways to Create a Custom Group
Option 1 – Use GROMACS Selection Syntax:
Use logical operations on existing groups. For example, to capture all non-C-alpha atoms in the protein, the selection string would be:
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1 |
"protein" & ! "C-alpha" |
You can test this string and preview the resulting selection in SAMSON.
Option 2 – Use SAMSON Graphical Selection:
For a more visual workflow, use SAMSON’s selection menus. For instance, you might want to define a group for neutral side chains in amino acids.
Select from the menu: Select > Residues > Amino acids > Side chain charge > Neutral.
After making your selection, click + in the index group list, and then Generate based on current selection in document. SAMSON will infer the GROMACS selection string for you and suggest a name for the group.
Once satisfied, click Add index group to the list, and then apply your changes. They’ll be saved in the index.ndx file in your project folder.
Conclusion
Adding custom index groups at the equilibration step balances flexibility and system completeness. All default index groups are available at this stage, and SAMSON’s interface makes it easy to define precisely what you need—whether through syntax or visual selection. This can save hours of debugging and ensures more accurate tracking during simulations.
Want more details or examples? Visit the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.