For many molecular modelers, the challenge begins once a system has been prepared: where do you find the computational power to run your molecular dynamics simulations? GROMACS is a fast and versatile engine, but preparing your system locally, worrying about hardware compatibility, or waiting hours for results can be a major bottleneck.
If you are a SAMSON user, there’s now a streamlined solution: the GROMACS Wizard Extension lets you run full GROMACS simulations directly in the Cloud, from within the same interface you use to design and prepare your molecular systems.
Why Use the Cloud?
Cloud computation means you’re not limited by the specs of your personal computer. Instead of queuing jobs locally or setting up a remote server manually, you can:
- Run simulations without installing or maintaining GROMACS separately
- Avoid overloading your computer while still working on other parts of a project
- Get results faster by leveraging distributed resources
Straightforward Setup
The GROMACS Wizard Extension ships with GROMACS 2021.3 by default, so you don’t need to worry about compiling or setting up different dependencies—it works out of the box. If you’d prefer to use a custom local version for optimization, that’s still supported. But importantly, for Cloud computing, everything is handled for you.
How Cloud Simulations Work in SAMSON
After preparing your system via the Wizard’s steps—pre-processing, solvation, minimization, equilibration—you’re ready to launch your production simulation. Here’s where Cloud functionality shines:
- From within the GROMACS Wizard interface, choose the ‘Cloud’ computation option.
- SAMSON will manage packaging your simulation files and submitting them to the Cloud.
- A notification will inform you once the job is complete, and the results will be available within SAMSON: trajectories, plots, and analysis-ready data.
It’s as integrated as it could get. No terminal commands, no external job schedulers, no emailing yourself trajectory files.
Common Use Cases
This feature is especially useful when:
- You need to run several simulations in parallel and don’t want to swamp your own machine
- Your local computer has limited memory or GPU resources
- You want to keep workflows centralized in one platform while still using powerful remote resources
You can find the Cloud option in the latter part of the tutorial series available here:
Launching computations in the Cloud
Where to Start
If you haven’t tried the GROMACS Wizard Extension yet, it can be added through the SAMSON Connect interface. Once installed, you’ll find it under Home > Apps > Biology inside SAMSON.
For full installation steps and detailed walkthroughs of each simulation stage, check out the GROMACS Wizard documentation page for a comprehensive guide:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and try the GROMACS Wizard Extension at https://www.samson-connect.net.