When designing molecular simulations, researchers often encounter the challenge of adequately analyzing specific parts of a molecular system. Standard index groups generated by GROMACS Wizard can sometimes fall short if a study requires tailored selections for detailed exploration. This is where the feature to add custom index groups in the preparation step truly stands out. Let’s dive into how this feature can streamline your simulation workflow and open up new analytical possibilities.
What are Index Groups?
Index groups are sets of atoms or residues defined to perform particular tasks in simulations, such as applying forces, measuring distances, or analyzing specific molecular regions (e.g., protein, solvent, or specific residues). By default, GROMACS prepares standard index groups like protein, solvent, or ions, but custom groups allow you to go beyond these predefined selections.
Why Add Custom Groups?
Custom index groups are crucial in simulations where certain subsets of molecules or residues require special attention, such as pull coordinate groups for umbrella sampling or residues with specific behaviors in your system. For example, one might need to monitor residues in alpha helices or study interdomain dynamics of a protein.
How to Add Custom Index Groups
Adding custom index groups is easy in the GROMACS Wizard:
- After specifying the molecular system and launching the preparation step, click the Add/edit index groups button.
- A pop-up window opens, allowing researchers to define and name new index groups. Selections can be made either using the GROMACS syntax or with SAMSON’s intuitive selection tools.
For instance, to create an index group for residues in alpha helices:
- Select residues representing alpha helices using SAMSON’s menu: Select > Residues > Amino acids > Secondary structure > Alpha helices.
- In the pop-up window, click the Generate based on current selection in document button. This will automatically produce a syntax-compatible selection for GROMACS based on your SAMSON selection.
- Name the new group (e.g.,
HELICES) and add it to the list by clicking Add index group to the list.
The result? Your custom group is now ready for use in subsequent steps like analysis or simulation debugging.
A Hands-On Example
Below is a visual example showing the interface for adding custom index groups and generating selections:
This example demonstrates how SAMSON simplifies the whole process by providing user-friendly tools that translate selections into GROMACS-compatible commands.
Note
Custom groups are stored in the index.ndx file within your project folder. They can also be modified during steps like minimization, equilibration, or simulation, giving flexibility throughout your workflow.
Conclusion
The ability to add custom index groups helps molecular modelers focus on their specific areas of interest, enabling deeper analyses and more precise simulations. Whether you’re investigating secondary structures, engaging in complex system interactions, or applying advanced constraints, this functionality ensures you have the right tools for the job.
To explore this feature further and see additional use cases, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.