Molecular modelers often need to run resource-intensive simulations, but not everyone has access to a powerful local machine or the time to configure cluster computing tools. Whether you’re working remotely, switching between different operating systems, or just trying to avoid frequent software installs, managing a GROMACS setup can be a hassle. This is where the GROMACS Wizard Extension for SAMSON can make a difference—particularly its built-in support for launching computations in the Cloud.
The GROMACS Wizard provides an integrated environment where users can prepare their molecular systems and launch GROMACS simulations directly in the Cloud. This makes it especially useful for users without local access to high-performance computing resources. It’s also helpful for beginners who may not be comfortable with the complexity of setting up simulation environments from scratch.
Here’s how it works:
From local setup to instant Cloud computing
Once you’ve installed the GROMACS Wizard Extension, your simulations can be run without installing or compiling GROMACS manually. Even better, the latest version of the extension comes with GROMACS 2021.3 prepackaged, so all you need to focus on is your science, not your software stack.
Within the extension, you’ll prepare your simulation in guided steps—starting from system setup, energy minimization, and equilibration to production dynamics. At every stage, instead of running the computation locally, you can choose to send it to the Cloud. This is particularly helpful for longer simulations that might otherwise block your local machine for hours (or days).
No command lines, no queues
Users often associate running GROMACS in the Cloud with command-line tools, scripts, submission queues, or navigating cloud service providers. The GROMACS Wizard bypasses all of this. The Cloud launch feature is built into the SAMSON graphical interface. You don’t need additional cloud accounts. Just configure your simulation and click to launch it.
This ease of access makes advanced molecular dynamics simulations available to a much wider range of users—from students in training environments to professionals working across different institutions or devices.
And when it’s done? Results are sent back to SAMSON in the form of trajectories and plots that you can immediately begin analyzing.
If you’re used to exporting results from a remote terminal and converting formats just to visualize them, this all-in-one integration will likely save you a significant amount of time.
Who is this for?
- Researchers with limited local computing resources
- Remote teams collaborating across OS platforms
- Students and educators needing practical simulation tools without system admin overhead
- Anyone wanting to quickly test and visualize molecular behavior before committing to longer calculations
Discover how cloud launch works directly from the documentation: Launching computations in the Cloud.
To explore the entire workflow and what the GROMACS Wizard Extension can do, visit the full documentation at https://documentation.samson-connect.net/tutorials/gromacs-wizard/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.