One common barrier in molecular dynamics simulations is limited local computing resources. Whether you’re working on a laptop or a shared desktop, the complexity of your system can easily outpace your hardware—especially during production runs. Fortunately, the GROMACS Wizard Extension for SAMSON presents a useful workaround: cloud-based GROMACS simulations, directly from within the SAMSON interface.
This extension integrates essential GROMACS simulation capabilities and adds cloud computation support. It means you can now offload demanding calculations to scalable cloud infrastructure—without managing configurations or setting up remote environments manually.
Why Run Simulations in the Cloud?
Here are a few reasons molecular modelers may want to consider this option:
- Hardware limitations: Not every machine is designed for long, intensive simulations.
- Scalability: Cloud access enables you to simulate larger systems or longer trajectories without worrying about memory or CPU limits.
- No installation headaches: The GROMACS package (version 2021.3) is already bundled with the extension, so there’s no need to install it yourself on the cloud environment.
- Remote workflow: Run simulations from virtually anywhere with just internet access and SAMSON installed.
How It Works
Once you install the GROMACS Wizard Extension, launching a simulation in the cloud is streamlined into a few steps:
- Prepare your system using the Wizard’s guided steps (from preprocessing to equilibration).
- Under the simulation settings, choose to run the job in the cloud.
- Submit your computations, and the extension takes care of cloud submission and results retrieval.
When the simulation completes, SAMSON provides access to the trajectory files and analysis plots, just like a local run. You won’t need to download any data manually or write scripts to sync results back.
Use Your Local GROMACS Build?
Some users may prefer to run highly optimized local GROMACS builds, especially if tailored to a specific GPU or HPC architecture. You can still do that—the extension supports using your local GROMACS version. But if performance or installation complexity is an issue, the cloud execution option becomes very attractive.
Supported Systems
The GROMACS Wizard Extension can be used on Windows, Linux, and macOS. Cloud simulations are just a click away, regardless of your local operating system.
Simplify Collaboration
For researchers working in teams, cloud-based simulations open up the possibility of reproducible and shareable workflows. Since system setup, configuration, and execution parameters are retained within the SAMSON environment, you can easily share your project with colleagues, who can then launch identical simulations or inspect results.
The GROMACS Wizard isn’t just about running GROMACS—it’s about making simulations more accessible, flexible, and integrated into your existing workflow.
To learn more about launching simulations in the cloud with the GROMACS Wizard Extension, head over to the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.