For many molecular modelers, managing simulation workflows can become complex when switching between tools, environments, and machines. If you’re using GROMACS for molecular dynamics, you probably know the challenges involved with setting up simulations locally: installation and compilation, environment configuration, ensuring GPU acceleration works, and occasionally dealing with out-of-memory errors on your personal machine.
If any of that sounds familiar, you might be interested in this: the GROMACS Wizard Extension in SAMSON includes the ability to launch and manage GROMACS simulations directly in the Cloud—no command-line gymnastics needed.
Why Run Simulations in the Cloud?
Local simulations come with certain limitations: hardware constraints, long runtimes, or the risk of tying up your machine for hours or days. Cloud simulations help offload intensive workloads while keeping your machine free for other tasks. More importantly, you can scale up with multiple runs and larger systems without worrying about how much RAM or GPU memory is available locally.
The GROMACS Wizard acts as an interface within SAMSON, allowing you to configure your system and run simulations in the Cloud. It handles the remote execution and automatically retrieves the results—including trajectories and plots—back into your local project, seamlessly.
How It Works
Once your molecular system is set up using the steps available in SAMSON (such as pre-processing, energy minimization, and equilibration), you can launch the production run in the Cloud. Here’s an overview of what happens:
- The extension packages your system and simulation parameters.
- It sends the package to the Cloud.
- The simulation is executed using a remote instance pre-configured with a compatible GROMACS build.
- Results are downloaded when the job is complete, including all output files and basic visualizations.
All of this is initiated from a graphical user interface—no scripting or remote login required.
Things to Keep in Mind
You don’t need to worry about installing GROMACS yourself; it’s shipped directly with the extension (currently GROMACS 2021.3) and can be run on Windows, Linux, or macOS. Even better, if you have your own optimized GROMACS build—say one compiled with a specific MPI version or GPU flags—you can still use that locally while benefiting from Cloud-based computation when needed.
Who Is This For?
This option is especially useful for:
- Researchers with limited access to high-performance local machines
- Students learning molecular simulation without experience in cluster computing
- Teams looking to prototype quickly without building infrastructure
The GROMACS Wizard makes the shift from local to Cloud almost invisible—you prepare your system using visual tools, skip the setup tedium, and focus directly on the science. Upgrading from local to remote simulations is a checkbox away.
You can explore all the steps involved in Cloud simulation (and more) in the GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.