If you’ve ever had to run the same molecular dynamics protocol across a set of conformations for a single molecule, you know how tedious it can be to duplicate setup steps, adjust box sizes, or ensure that each conformation is initialized correctly. This repetition not only increases the chance of inconsistencies, but it also wastes precious modeling time.
The GROMACS Wizard in SAMSON provides a powerful solution with its batch preparation mode. It allows you to prepare a whole series of simulations—in one go—starting from multiple conformers of the same molecular system. Whether you’re conducting umbrella sampling or analyzing dynamic variability across different conformations, this feature could save you hours of manual setup.
What’s the Use Case?
Let’s say you have a protein and want to run MD simulations starting from various initial conformations, for example, snapshots from a previous simulation, docking poses, or a static ensemble produced by another plugin. Instead of preparing each simulation individually, you can treat the conformations as subprojects within a single batch project.
How It Works in SAMSON
Here’s how SAMSON helps facilitate this workflow:
- Load your conformations into SAMSON. These could be:
- Imported from a trajectory,
- Generated using tools like Twister, Ligand Path Finder, or Python scripts,
- Extracted selectively by frame for finer control.
- Select your conformations or a complete path (trajectory) in the Document view.
- Enable batch preparation mode in the GROMACS Wizard’s Prepare tab by checking the appropriate box.
- Assign the selected conformations. Each frame or conformation becomes an individual subproject with its own trajectory and parameters—but inherits setup preferences from the global batch.
Defining the Periodic Box (and Why That Matters)
If you’ve experienced mismatched box sizes across similar systems, you’ll appreciate the ability to define the simulation box either:
- Based on all conformations (consistent sizing across subprojects), or
- Individually per conformation (slightly tighter boxes for compact states, reducing computational overhead).
Both options follow best practices for minimum image convention and give you control over space vs. performance tradeoffs.
One Click to the Final Steps
Once your conformer-based batch is prepared, simply proceed with batch execution for minimization, equilibration, and production MD. Local and cloud options are available. Each conformer will proceed in parallel through the chosen workflow stages. Depending on your configuration, this can significantly reduce resource consumption and simplify job management.
Why Modelers Like This Workflow
- ✅ No more repetitive setup for each conformation
- ✅ Consistent parameters across a full batch
- ✅ Clear organization: One folder per subproject, easy to manage
- ✅ Prepares you for workflows like umbrella sampling, ensemble modeling, or parameter scanning
This setup makes it easy for you to stay focused on your modeling questions rather than setup logistics.
Learn more in the full GROMACS Wizard – Batch Computations guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.