If you work in molecular modeling, you’ve likely encountered this issue: you’d like to run a GROMACS simulation, but you’re either working on a laptop with limited resources, or you just don’t want to spend time installing and maintaining GROMACS on your machine. Whether you’re on Windows, Linux, or macOS, setting up high-performance software like GROMACS can be time-consuming—and it’s not always straightforward.
Fortunately, there’s a way to skip the setup and still get the full power of GROMACS—by running your simulations in the cloud using the GROMACS Wizard Extension for SAMSON.
Cloud Simulation with GROMACS Wizard
The GROMACS Wizard Extension integrates GROMACS into SAMSON, a platform for integrative molecular design. It not only allows you to run simulations locally, but also lets you launch them directly in the cloud. This means you can:
- Bypass the complexity of installing and compiling GROMACS
- Access more computing power than your local machine may offer
- Keep your local resources free while the simulation runs elsewhere
Cloud computing might sound like a setup challenge in itself, but the GROMACS Wizard makes it seamless. Once installed inside SAMSON, you just click through to the cloud option and let the rest happen behind the scenes.
Why Use the Cloud?
This feature is particularly helpful for users who:
- Are working from laptops or shared devices
- Run frequent simulations and want to save time on setup
- Prefer not to worry about software dependencies or upgrades
- Want to scale up simulations without investing in hardware
How It Works
The GROMACS Wizard interface is fully integrated into SAMSON’s workspace. Once your molecular system is prepared, simply choose the cloud option during the setup process. The software packages everything and launches the computation remotely. You can continue working on other tasks or shut down your computer while the cloud-based simulation completes.
When the simulation is done, results such as trajectory files and plots are sent back to your local environment, where you can analyze and visualize them within SAMSON.
Getting Started
To use this feature, install the GROMACS Wizard Extension from the SAMSON Extensions marketplace. Make sure you are signed in to your SAMSON Connect account. Then simply follow the process described in the documentation to launch remote simulations.
Note: You are not limited to using the built-in version of GROMACS. The extension ships with GROMACS 2021.3, but if you’d rather use your own version for compatibility or performance, you can specify that too.
To learn more about launching simulations in the cloud, including example setups and tips, check out the full documentation here: 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.