If you’ve ever run molecular dynamics simulations for multiple conformations of the same molecule, you know how tedious it can be to repeat the same setup steps over and over. Whether you’re iterating through a ligand binding pathway or comparing structural variants, manually preparing simulations for each case is costly in both time and focus.
The GROMACS Wizard in SAMSON offers a way to streamline this process through batch computations. With just a few clicks, you can prepare full simulation projects for every conformation in your dataset—automatically.
What’s a Batch Project?
In SAMSON, a batch project is a set of simulation projects generated from either:
- a set of conformations (e.g., saved states from docking or conformational sampling), or
- a path (e.g., from an animation or a trajectory)
Each conformation or frame becomes the starting point for an independent project, fully set up for simulation, with its own subfolder and configuration.
Why Use Batch Projects?
- Save time by automating redundant setup tasks.
- Ensure consistency across simulations.
- Run everything locally or in the Cloud with ease.
How to Prepare a Batch Simulation
You can start from an existing trajectory or generate conformations using SAMSON editors or other extensions like AutoDock Vina Extended, Normal Modes Analysis, or protein-protein docking with Hex.
After you have your conformations:
- Open the Prepare tab in the GROMACS Wizard.
- Activate the [Optional] Batch project checkbox.
- Choose either a set of conformations or a path.
- Click Set conformations or a path.
You’ll see a slider that lets you browse through the loaded conformations, and confirmation of how many will be used.
What About the Simulation Box?
One useful feature is the ability to choose how simulation boxes are defined for the batch:
- One shared size for all conformations using “Box lengths”, helpful when you want consistency between simulations.
- Individual size per conformation using “Solute-box distance”—ideal if you’re trying to optimize performance and some conformations are more compact than others.
Ready to Simulate
After batch preparation, you can proceed with:
- Energy minimization
- NVT and NPT equilibration
- Production runs
Each subproject can be run independently, locally, or in the Cloud. Local executions appear as separate jobs in the Local jobs window, where you can track their status, re-order them, or stop any ongoing run.
Final Thoughts
Batch simulations in SAMSON drastically reduce the overhead of high-throughput molecular dynamics projects. If you’ve ever wanted a more structured way to simulate multiple conformations, this feature is worth trying out.
Learn more about batch computations in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.