A simulation setup can be technically ready and still be missing one small, important thing: the exact atom or residue group needed for a pull coordinate, a focused analysis, or another workflow step. Rebuilding a system just to define that group is frustrating—and adding it at the wrong point can make the selection harder than it needs to be.
In SAMSON’s GROMACS Wizard, custom index groups are added through the selection tools you already use in SAMSON or by entering GROMACS selection syntax. The key decision is when to create them. Choose the preparation step when the same custom groups should be available across a batch of subprojects. Choose equilibration or simulation when the group depends on standard index groups that GROMACS creates during preparation.
Choose the right point in the workflow
For a single system, you can add groups during preparation, equilibration, or simulation. Preparation is convenient when you want to define groups once and carry them into later stages. It is also the recommended point for a batch project, so the group creation happens once for all subprojects.
There is a trade-off: at preparation time, the default GROMACS-generated index groups are not yet available. If your custom selection relies on those groups, wait until equilibration or simulation, after preparation has generated them. At those later steps, load the system in SAMSON if it is not already loaded, then open Edit index groups.
Build groups from selections you can inspect
The index groups window lists the default groups generated by GROMACS. They cannot be modified there, but you can inspect which nodes they correspond to by using Select in document based on selection string. The groups are also available in the document folder; double-clicking one selects its corresponding atomic structures.
To create a group, click + below the group list. You can enter a GROMACS selection string directly, or first make a selection in SAMSON and choose Generate based on current selection in document. SAMSON then generates the corresponding selection string. This is useful when your intended group is easier to identify visually or with SAMSON’s selection mechanisms than to express manually.
For example, the tutorial demonstrates selecting amino-acid residues with neutral side chains through Select > Residues > Amino acids > Side chain charge > Neutral. Once selected, generate the group from the current document selection, give it a meaningful name, and click Add index group to the list.
Validate before relying on the group
Whether you write the selection string yourself or generate it from a SAMSON selection, check what it selects before using the group downstream. The window provides Test selection string and Select in document based on selection string, so you can compare the result against the intended atoms or residues. This check is especially important if residue or atom numbering is unusual.
There is a specific caution for groups created during preparation: systems with non-unique or non-consecutive residue or atom indices can sometimes lead to indexing issues. Verify the generated groups afterward. For a single project, creating the group at equilibration or simulation is an alternative when that fits the workflow.
Finally, click Apply to save changes. The groups are added using gmx make_ndx and stored in the project’s index.ndx file. A clear group name and a quick selection check can save confusion when you return to the project or use the group in a later step.
For the full procedure and related workflow links, see the GROMACS Wizard guide to adding custom index groups.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.