Molecular simulations often involve repetitive workflows, such as energy minimization, equilibration, and molecular dynamics across multiple conformations or systems. Configuring these setups manually for every iteration can be time-consuming – especially if dealing with dozens or hundreds of starting points! Fortunately, SAMSON’s GROMACS Wizard offers a solution: batch computations. This feature enables efficient handling of repetitive simulation setups and computation management, saving valuable time for molecular modelers.
Why Use Batch Computations?
If you’re running similar GROMACS workflows on multiple conformations of a single molecular system or a set of different systems, batch mode is your best friend. Instead of configuring each project individually, batch mode automates the process. Whether you’re analyzing a protein with multiple folding states or comparing simulation results across several molecular systems, batch mode simplifies the workflow.
Getting Started with the GROMACS Wizard Batch Mode
Here’s how you can streamline your projects using batch computations with SAMSON:
1. Preparing Your Batch
A Single Molecular System: Start by preparing a single system with multiple conformations. You can either load an existing trajectory (Home > File > Open or Ctrl/Cmd + O) or create conformations directly within SAMSON. Tools like Move editors and Twister are great for generating conformations.
Multiple Molecular Systems: Prepare each system individually, ensuring consistent simulation settings for all. Gather these prepared systems into a single “batch” folder for shared processing.
2. Define Preparation Workflow in the GROMACS Wizard
Once your conformations or systems are ready:
- Open the Prepare tab in the GROMACS Wizard.
- Select your molecular system and check the [Optional] Batch preparation box.
- Input your conformations or paths as initial frames for each subproject in the batch. For flexible batch configurations, you can choose between options like a set of conformations or a path (trajectory where each frame represents a simulation state).
- Define parameters like the force field, solvent, and periodic box. Helpful guidance is available in resources such as Step 1: Prepare.
3. Periodic Box Settings
Batch mode also lets you define periodic boxes efficiently, either by considering all conformations collectively (via Box lengths) or setting it per conformation (via Solute-box distance). This flexibility helps balance accuracy and computational efficiency.
Tip: Once set, slide through your conformations in the “Batch preparation” tab to check how the periodic box fits each structure.
4. Launching Your Batch Project
After preparation, you can kick off the next steps of the simulation workflow: minimization, equilibration, and production runs. Use From batch folder as the input path during these steps. Batch computations can be executed locally or in the cloud, depending on your resources and preference.
For local execution, each subfolder in the batch will correspond to a separate job, visible in the Local jobs window. You can monitor, pause, or reprioritize jobs here. For cloud-based execution, similar controls are available in the Cloud jobs window.
When to Use Batch Computations?
Batch computations shine especially when:
- You’re performing umbrella sampling, which can involve multiple conformations of a single system.
- You’re simulating a series of proteins or molecular systems using consistent parameters.
- Efficiency and reproducibility are major priorities in your simulation workflow.
Learn More
Ready to dive deeper? Check out the detailed documentation on batch computations at this link.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit SAMSON Connect.*