For many molecular modelers, setting up a GROMACS simulation often starts with the same familiar workflow — downloading GROMACS, compiling it, troubleshooting library issues, and repeating the cycle on different machines or operating systems. It’s a time-consuming process that can become a frustrating barrier, especially when managing multiple simulations or collaborating in groups.
But there’s a way to skip the entire setup. The GROMACS Wizard Extension for SAMSON offers cloud-based simulation, including pre-installed GROMACS support. This means no compilation, no dependency wrangling, and no configuration headaches — just upload your system, set parameters, and simulate directly in the cloud. Whether you’re using Windows, Linux, or macOS, it works out of the box.
How It Works
The GROMACS Wizard Extension integrates key GROMACS functionalities within SAMSON. With this extension, you can:
- Prepare your system directly in SAMSON using a graphical interface
- Choose to run your simulation locally or in the cloud
- Access results — trajectories, energies, plots — directly from the interface
When you choose to run a simulation in the cloud, SAMSON handles submission and monitoring, while you retain full control over which operations to perform — energy minimization, equilibration (NVT/NPT), or full production molecular dynamics.
When Cloud Becomes Useful
Cloud-based simulations in SAMSON are especially useful in situations like:
- Working on lightweight systems (laptops): Avoid long runtimes or overheating your device
- Running multiple simulations: Quickly test different parameters or system configurations in parallel
- Collaborating remotely: Avoid version discrepancies by enabling team members to use a consistent build instantly
SIMULATIONS can be launched with just a few clicks. You don’t even need to install GROMACS yourself — the extension ships with GROMACS 2021.3, but also allows you to switch to your own local version if needed (for example, to access a GPU-accelerated build).
One Less Problem to Solve
Removing the need to compile and configure GROMACS helps you focus more on science and less on setup. If you’ve been delaying simulations because of technical barriers, using SAMSON’s GROMACS Wizard might just remove that friction.
Here’s what the interface looks like:
To start using the GROMACS Wizard and run cloud simulations, sign in and install the extension via the SAMSON Connect site. Once installed, it’s automatically integrated into your SAMSON interface.
Learn more about how it works and what else you can do with it in the full documentation: 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.