Molecular modelers often face the time-consuming task of running identical simulations on multiple molecular systems or conformations. From umbrella sampling to comparing protein structures, this repetitive setup can feel daunting and error-prone. Enter the GROMACS Wizard Batch Computations feature, designed to streamline this process and free up valuable time for deeper analysis.
Why Use Batch Computations?
Batch computations provide a handy way to apply identical GROMACS workflows to numerous initial states or molecular systems. Whether you’re working with a single molecular system with multiple conformations (e.g., umbrella sampling) or a set of completely different systems (e.g., proteins sharing the same parameters), this feature eliminates the need for repetitive manual configuration.
Here’s a closer look at how you can use batch computations for a single system with many conformations:
Preparing Conformations for Batch Processing
Before diving into batch processing, you’ll need to ensure your molecular systems or conformations are ready. For instance, if you’re examining multiple conformations of a single system, you can:
- Import existing trajectories: Simply use
File > Open(Ctrl/Cmd + O) or drag and drop a trajectory file into SAMSON. - Create conformations: Leverage tools built into SAMSON such as editors (e.g., Twister) or other extensions (e.g., Normal Modes Analysis), or even convert animations into paths.
Want a specific subset of trajectory frames? Use the Inspector to filter and export specific frames as individual conformations or modify an entire trajectory and delete unnecessary frames. The ease of these features makes working with batch processes more targeted and efficient for your research needs.
Setting Up Batch Preparation
Once your conformations are ready, navigate to the GROMACS Wizard’s Prepare tab. The key steps include:
- Select initial conformations: Choose either a single trajectory file (path node) or a set of conformations for the batch computation. Each frame or conformation acts as an initial state for subprojects.
- Set force fields, solvents, and index groups: These simulation essentials are applied uniformly across all subprojects.
- Define a periodic box: You can decide whether the box size should be consistent across all conformations or adaptable per conformation. Both methods ensure compliance with the minimum image convention.
When you’re ready, click Prepare. The result is a batch project organized into subfolders, each representing a separate, ready-to-run molecular system. This hierarchical organization makes subsequent steps—minimization, equilibration, and molecular dynamics simulation—a breeze to execute, whether locally or in the cloud.
Batch Simulation Output
After preparation, the workflow mirrors that for a single project. Each subfolder can undergo minimization, NVT equilibration, NPT equilibration, and production molecular dynamics simulation. The flexibility of launching simulations locally or in the cloud ensures compatibility with different computational setups. Local jobs can be prioritized and managed in the Local jobs window, while cloud jobs are trackable in the Cloud jobs window.
Whether you’re running umbrella sampling or comparing a batch of proteins, this feature simplifies a previously tedious process. To get started on your next batch computation, visit the full tutorial here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.