For molecular modelers, running a GROMACS simulation often comes with a big technical prerequisite: installing, compiling, and configuring everything correctly on your local machine. This can take hours—and might involve battling with dependencies, GPU compatibility, or queuing systems. What if you could skip all that and just launch your simulations directly in the Cloud, with a couple of clicks?
The GROMACS Wizard Extension in SAMSON offers exactly this capability. With built-in support for GROMACS 2021.3, it allows you to manage all the standard steps of a molecular dynamics simulation—preparation, minimization, equilibration, and production—without ever needing to leave your graphical interface, or even run the computations locally.
What problem does this solve?
Many researchers and students interested in exploring molecular systems face a key bottleneck: inadequate local computational resources. Laptops or desktops may not have adequate performance for long simulations, or they might lack a proper GROMACS installation. Even seasoned computational chemists may not want to duplicate or reconfigure environments across systems.
By enabling seamless Cloud execution, the GROMACS Wizard in SAMSON removes these limits. You don’t need to compile GROMACS, install prerequisites, or manage environment modules. You prepare your system, select Cloud compute, and hit launch.
How does it work?
Once you’ve prepared the structure and set your simulation parameters using the Wizard interface, go to the Cloud launch section. Instead of selecting “run locally,” you choose the Cloud run option. SAMSON takes care of packaging your inputs, transferring them to a remote computing environment, running the specified GROMACS operations, and bringing back your outputs—just like if you had run it on your machine.
Results appear in the GUI as trajectories and plots, so you can analyze everything in SAMSON. Output files can also be exported for external visualization or publication needs.
Use cases where this helps
- Students and educators working on shared or low-performance machines can explore real MD workflows without setup hurdles.
- Early-career researchers experimenting with new protocols can quickly prototype simulations from anywhere.
- Cross-platform users (e.g., Mac users for whom native GROMACS support is more limited) can access full simulation capabilities.
How to try it?
If you already have SAMSON installed, simply sign in to add the GROMACS Wizard Extension. It includes the GROMACS engine, so you don’t need to download or configure anything else. To use Cloud simulation features, choose the Cloud option in the simulation setup stage of the GROMACS Wizard workflow.
There is no extra charge to try these features—the Wizard and SAMSON are accessible after a simple sign-up. It works on Windows, Linux, and MacOS systems.
To learn more, visit the full GROMACS Wizard tutorial documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.