Performing molecular simulations often involves managing multiple conformations or preparing different molecular systems. This can be an overwhelming and tedious task when done manually. Fortunately, the GROMACS Wizard in SAMSON simplifies these processes through batch computations, allowing molecular modelers to streamline their workflow and focus on the science rather than repetitive setup tasks.
Why Use Batch Computations?
Batch computations are particularly useful when you need to perform simulations on:
- A single molecular system with multiple conformations (e.g., umbrella sampling).
- A set of different molecular systems, such as various proteins, with the same parameters.
By automating the preparation, minimization, equilibration, and simulation steps for multiple systems or conformations, you save time and reduce the risk of errors. You can run these computations locally or in the cloud, boosting efficiency for resource-intensive tasks.
Getting Started with Batch Computations
To begin, you’ll need an existing trajectory or set of conformations. You can load your data into SAMSON via:
- Home > File > Open (Ctrl/Cmd + O)
- Drag-and-drop functionality
Alternatively, leverage SAMSON’s tools to generate trajectories or conformations. For example:
- Editors like Twister or the Move editor.
- Extensions like Normal Modes Analysis or Ligand Path Finder.
- Path-based conformations via Path > Create conformations from path in the context menu.
Additionally, export specific trajectory frames using the Inspector or create a large set of conformations and later remove the ones you don’t need.
Preparing for Batch Projects
Once your data is loaded or created, follow these steps to set up a batch project:
- Open the Prepare tab in the GROMACS Wizard.
- Set the molecular system by selecting a structural model in the Document view.
- Enable [Optional] Batch preparation to specify initial conformations or a path:
- Select a set of conformations where each acts as an initial state for a subproject.
- Choose a path where each frame acts as a subproject’s initial state.
- Define other parameters such as the force field and solvent.
- Specify ion concentrations and set up the periodic box (same for all conformations or individual for each).
After clicking Prepare, SAMSON organizes the batch as numbered subfolders, each representing a separate project.
Launching and Managing Batch Computations
Once the batch project is prepared, you can perform the following steps:
- Energy minimization
- NVT equilibration
- NPT equilibration
- Production Molecular Dynamics simulation
Choose From batch folder as the input path. The computations can be launched locally or in the Cloud. For local computations, jobs are accessible in the Local jobs window, where you can monitor progress, adjust priorities, or cancel tasks. For Cloud computations, results can be managed through the Cloud jobs window. This flexibility ensures that computational resources are used efficiently, whether on a personal workstation or in the Cloud.
Conclusion
Batch computations with the GROMACS Wizard simplify repetitive tasks in molecular design, supporting efficient preparation and simulation for multiple systems or conformations. To explore all features and advanced options, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON by downloading it from here.