Running molecular dynamics (MD) simulations for a variety of protein systems often comes with a familiar headache: reproducibility and consistency across runs. 🧠Whether you’re screening mutations, comparing homologs, or simply evaluating binding dynamics across different proteins, ensuring that all systems are prepared, minimized, equilibrated and simulated with identical protocols can quickly become time-consuming.
The GROMACS Wizard within SAMSON offers a useful solution to this challenge through its batch computation feature for a set of different systems. Instead of preparing and running every simulation separately—hoping you didn’t forget a critical flag—you can automate the workflow to process all systems with shared parameters, including in the cloud. Here’s how it works.
Why batch processing matters
Running simulations for multiple systems (different proteins, for instance) typically involves repeating the exact same setup pipeline manually: configure a periodic box, ionize the system, minimize energy, equilibrate (NVT, then NPT), and finally run production MD. But any inconsistency—different solvation models, different index groups, misplaced folders—can lead to invalid comparisons.
The batch function simplifies this by treating each protein system as a subproject and allowing you to run all steps across multiple independent folders within a single streamlined workflow.
How to prepare a batch of protein systems
- Prepare each system separately: Use SAMSON’s GROMACS Wizard to run the preparation step on each protein. You can add a force field, solvent, ions, and define the periodic box. Each resulting folder will have a “-prepare” suffix.
- Organize in a batch folder: Create a new “batch” folder and drag all the “-prepare” folders into it. Each folder represents a prepared protein system. Rename them if desired (e.g., by PDB ID), but it’s optional.
- Load from batch folder in later steps: For subsequent steps like energy minimization and equilibration, simply choose “From batch folder” as the input. The wizard will automatically process each folder using the same set of parameters.
This is particularly useful when running in the cloud, where each system will generate a separate cloud job managed independently. For local computations, each becomes a separate local job that can be prioritized or stopped as needed.
Important notes
- Index groups and restraints: Avoid using system-specific index groups or position restraints unless you’re working on advanced simulations. These should remain consistent across systems.
- Consistent protocols enable comparison: Whether you’re testing drug binding across variants or comparing folding behavior among proteins, this approach ensures you’re comparing apples to apples.
Inputs and output management
Each subfolder in your batch behaves like a standalone MD project. You can access job status, download results, and even visualize trajectories, all while knowing that your input parameters were applied uniformly.
To learn more about the batch setup for different systems in GROMACS Wizard, visit the full documentation here:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/batch-computations/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.