One of the most time-consuming tasks for molecular modelers is setting up repetitive molecular dynamics workflows for multiple conformations or systems. Whether you’re handling a single system with several conformations or a batch of different systems, the manual configuration of each project can be tedious and error-prone. Fortunately, the GROMACS Wizard in SAMSON offers a powerful solution: batch computations.
Why Use Batch Computations?
Batch mode allows you to automate repetitive workflows across multiple starting states or related systems. This is especially useful for tasks like:
- Simulating a single molecular system with a set of initial conformations. For example, you can use this to perform umbrella sampling by running the same simulation across different conformational states.
- Processing a set of different molecular systems with the same parameters, like studying a group of proteins with uniform simulation settings.
This tutorial will guide you through working with batch computations in GROMACS Wizard, helping you save time and increase efficiency while maintaining consistency across projects.
Preparing for Batch Computations
If you’re working with multiple conformations of a single system, you can begin by loading an existing trajectory into SAMSON. SAMSON supports trajectory import via Home > File > Open (Ctrl/Cmd + O) or drag-and-drop. Alternatively, you can generate trajectories or conformations directly within SAMSON using various tools, such as:
- Move editors, like Twister.
- Extensions like Normal Modes Analysis or Protein-Protein Docking with Hex.
You can also isolate specific frames of a trajectory to use as initial conformations by exporting them directly in SAMSON, ensuring you have complete control over the starting states of your batch computations.
Setting Up Batch Computations
Once your conformations or systems are ready, proceed to the Prepare tab in the GROMACS Wizard:
- Set the molecular system: Choose a structural model from the Document view and set it as your system.
- Enable Batch Preparation: Check the “[Optional] Batch preparation” box in the setup wizard.
- Specify Conformations: Select a set of conformations or a trajectory path. Each conformation or frame will act as a separate subproject.
- Prepare the System: Configure force fields, solvents, and other parameters through the preparation steps, and finalize by clicking the Prepare button.
The result is a structured batch project containing numbered subfolders, each representing a separate simulation-ready system.
Defining the Periodic Box
For batch projects, you have two main options to define the periodic box:
- Box Lengths: Set a consistent box size across all conformations, ensuring alignment and uniformity.
- Per Conformation: Base the box size on solute-box distance for each conformation, reducing computational requirements for compact conformers.
Using the Batch preparation slider, you can visualize how the periodic box fits each conformation and adjust parameters as needed.
Scaling Up: Simulations in Batch
After setting up your batch project, you can seamlessly proceed to energy minimization, equilibration, and production molecular dynamics simulations. GROMACS Wizard supports launching batch computations both locally and in the Cloud:
- Local Computations: Jobs are managed individually through the Local Jobs window, allowing you to track progress, prioritize, and import completed work.
- Cloud Computations: Each subfolder in your batch is processed as a separate Cloud job, which can be monitored and managed from the Cloud Jobs window.
Conclusion
Batch computations in SAMSON’s GROMACS Wizard drastically reduce the manual effort required to set up repetitive workflows, enabling molecular modelers to focus on their science instead of logistics. To learn more, visit the full documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at SAMSON Connect.