Running molecular dynamics (MD) simulations can take a significant toll on local hardware, especially when simulating large systems or running long trajectories. Many researchers face the challenge of not having access to high-performance computing infrastructure when they need it most.
For those using GROMACS, one common pain point is relying on limited local resources, which can lead to longer runtimes, frequent crashes, and reduced productivity. Fortunately, the SAMSON GROMACS Wizard now offers an option to offload GROMACS computations to the Cloud — all from within the SAMSON environment and without needing to set up external clusters or cloud VMs manually.
Who Might Benefit From This?
If you’re a molecular modeller who:
- Works on a laptop or low-spec desktop and struggles with simulation jobs running locally
- Needs to test structures quickly without committing to full simulation jobs on supercomputers
- Wants a reliable way to start, monitor, and store simulation runs in a cloud workflow
…then using SAMSON’s built-in Cloud support for GROMACS via the GROMACS Wizard could streamline your workflow.
How Simple Is It?
Setting up a GROMACS job in the cloud takes just a few steps:
- Click Equilibrate in the cloud or Simulate in the cloud based on the step you’re running (e.g., NVT Equilibration).
- Choose the machine type from a pre-configured list with options for performance and cost — no GPU required for simple or test simulations.
- Confirm the job and monitor its progress in the Job manager.
Monitoring & Control
Once the simulation starts, you can monitor status updates, performance, and progress through the Job Manager. You can even pause or cancel the job as needed — all while continuing other work in SAMSON or even closing the application. Results stay stored in the cloud until you decide to download or delete them.
What Happens When the Simulation Completes?
When a job completes, you receive a notification. Then, you can download the results directly within SAMSON:
- Download individual or all result files
- Open them in external viewers or import directly into the GROMACS Wizard
- Continue to the next step in the simulation workflow (e.g. use an equilibrated GRO file for production MD)
It’s Modular
Since each step, like NVT Equilibration or Production MD, uses the same cloud interface, it’s easy to incrementally build your full simulation pipeline. Early-stage problems (e.g., instability) can be addressed by trying short local jobs or test runs before opting for longer cloud computations.
Why This Matters
Instead of spending time setting up remote servers, dealing with environment variables, or configuring GROMACS for the cloud manually, SAMSON simplifies the entire process into an integrated workflow. For education or research projects, it also provides transparency in cost (via credits) and complete control over job lifecycles—all from a single interface.
To learn more about using the GROMACS Wizard in the cloud, check out the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.