If you’ve ever had to run a Molecular Dynamics (MD) simulation for more than one conformation of a molecule, you’ve probably felt the pain of repetition: preparing each system individually, applying the same settings again and again, and tracking multiple simulation outputs. It’s time-consuming and easy to make mistakes. Fortunately, if you’re using SAMSON with the GROMACS Wizard extension, SAMSON has an answer: batch computations.
This blog post will walk you through the essentials of setting up batch simulations in SAMSON. The workflow lets you apply the same simulation protocol to multiple conformations of a molecular system in an organized, reproducible way. It can reduce the friction in your modeling process—whether you’re comparing docking results, assessing flexibility, or just exploring a conformational ensemble.
Why batch computations matter
Simulating multiple conformations can help with questions like:
- How does binding affinity vary across docked poses?
- Are some conformations more stable energetically than others?
- How does solvation affect conformational preference?
Answering these questions often requires running the same MD protocol many times—and that’s where SAMSON’s batch project support becomes invaluable.
Step-by-step: preparing a batch project in SAMSON
Everything starts with generating or loading a set of conformations. You can obtain these via:
- A trajectory loaded in SAMSON
- Results from tools like AutoDock Vina Extended or Normal Modes Analysis
- Animations created in SAMSON (e.g., undocking motion)
If needed, you can filter or select desired conformations:
- Use the Inspector to manually create conformations for selected frames.
- Generate conformations from an entire path and delete the ones you don’t need.
Enable batch mode
Open the Prepare tab in the GROMACS Wizard and check the box labeled [Optional] Batch project. Now, you’ll assign either:
- A set of conformations – each conformation becomes a subproject
- A path – each frame in a path becomes a subproject
Click Set conformations or a path once your selection is ready. You’ll notice a conformation slider appears, letting you preview each state.
Define the periodic box
For batch projects, you can set the simulation box:
- Same size for all conformations – use Box lengths.
- Per conformation – use Solute-box distance (recommended ≥1 nm).
Smaller boxes per conformation can reduce computing time. Use the box slider to preview how the periodic box fits each conformation:
Continue with GROMACS steps
Once everything is set, you can proceed with the usual GROMACS workflow under the same batch structure:
- Energy minimization
- NVT equilibration
- NPT equilibration
- Production MD
Choose the batch project as your input. If rearranging is needed, SAMSON’s local jobs manager gives you full control over priorities and execution:
Whether you’re running simulations locally or using the Cloud, each subproject is treated independently, making it easier to manage results and accelerate comparisons.
Conclusion
Batch computations in SAMSON’s GROMACS Wizard offer molecular modelers a robust way to reduce labor and increase reliability in workflows that involve multiple conformations. It’s especially useful for docking studies, conformational sampling, and exploring structural variability under identical conditions.
To learn more and access the full tutorial, visit the official documentation: GROMACS Wizard – Batch Computations.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.