For many molecular modelers, running large-scale GROMACS simulations is limited by local computing power. Long simulations, memory-heavy systems, or multiple production runs for enhanced sampling can all push the limits of a typical workstation. Cloud computing has emerged as a scalable solution — but setting it up manually, especially for GROMACS workflows, can be a challenge.
SAMSON’s GROMACS Wizard Extension simplifies this process by providing a direct, user-friendly gateway to launch GROMACS simulations in the Cloud, without requiring users to install or configure cloud environments themselves.
Why Use the Cloud for GROMACS?
- Bypasses the limitations of local hardware
- Enables batch simulations or parameter sweeps to run in parallel
- No need to install or configure GROMACS on your machine — it ships with the extension
- Frees up your desktop for other tasks while simulations run remotely
How It Works in SAMSON
The GROMACS Wizard integrates cloud launching directly into the SAMSON interface. You design and prepare your system using the Wizard’s guided steps, just as you would for a local run. Once your system is set for production, you can switch to the Cloud option and submit your job to remote resources.
This is what makes it approachable: there is no need for users to configure virtual machines, upload files to remote servers manually, or handle command-line environments. The interface remains visual, and cloud submission becomes, effectively, just another simulation step.
Cloud Setup Options
While the extension comes with a built-in GROMACS 2021.3 version ready to be used in the Cloud, advanced users can still configure their own GROMACS builds, even in cloud runs. This is valuable if your research requires custom builds with specific flags or libraries.
Use Case Highlights
Launching in the cloud is particularly useful when:
- You need to run multiple independent MD simulations for statistical sampling
- Your system contains several hundred thousand atoms and won’t run efficiently on a local laptop
- You want to keep your local resources free for visualization and analysis work
How to Get Started
To use this feature, first install the GROMACS Wizard Extension from SAMSON Connect. After system setup using the Wizard (steps 1 to 4), choose the “Launch in Cloud” option under the production step or in the final simulation submission dialog.
Job results — including trajectory files and standard GROMACS output — are automatically retrieved for visualization and further analysis within SAMSON.
This way, you can scale up your molecular dynamics simulations without scaling up your hardware.
To learn more about GROMACS simulations in the Cloud using the SAMSON GROMACS Wizard, visit the full tutorial at 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.