Running molecular dynamics simulations has never been more accessible—until it’s time to install, compile, and configure tools like GROMACS on your personal machine. This often becomes a time-consuming process, especially when working across multiple operating systems or hardware environments. For students, researchers, and professionals who just want to simulate and analyze molecular models, hours spent debugging installation issues can be frustrating.
The GROMACS Wizard Extension for SAMSON offers a solution many molecular modelers will appreciate: effortless access to GROMACS, including the ability to run simulations directly in the Cloud. This blog post walks through why this matters, and how the feature works in practice.
Why consider the Cloud?
Imagine you need to perform a set of production MD simulations but your local hardware isn’t optimized for this task. Or perhaps you’re working remotely, switching between a desktop, a laptop, and a shared lab computer. Using Cloud simulations gives you hardware independence, eliminates installation issues, and lets you access results from anywhere via your SAMSON account.
What the GROMACS Wizard Extension provides
The GROMACS Wizard is an extension in SAMSON, a molecular design software that integrates simulation, modeling, and analysis tools. This extension integrates core features from the GROMACS package, including system preparation, energy minimization, equilibration, production dynamics, and even analysis like PMF and umbrella sampling.
What’s especially helpful is that the extension includes a pre-installed version of GROMACS 2021.3. That means there’s no need to compile GROMACS or worry about compatibility—everything works out-of-the-box.
How Cloud integration works
Launching computations in the Cloud through the GROMACS Wizard is optional and can be done when needed. Here’s how a typical Cloud simulation workflow looks like:
- Prepare your system locally using the GROMACS Wizard in SAMSON
- At any stage (energy minimization, equilibration, production), choose to run the simulation in the Cloud
- View result files (trajectories, plots, logs) within SAMSON after completion
This is particularly useful for batch jobs, or for long production simulations you don’t want to occupy your local machine.
Visual preview
Here’s a preview of how the extension looks inside SAMSON:
Compatibility
The extension is available on Windows, Linux, and MacOS. Files and models can be transferred between systems seamlessly via SAMSON’s user account syncing.
Final thoughts
If you’re tired of managing simulation environments on different machines or simply want to start simulating with minimal setup time, Cloud integration in the GROMACS Wizard might save you hours. Best of all, your simulations remain reproducible and portable across devices.
Learn more in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.