Setting up and running molecular dynamics (MD) simulations can be time-consuming and computationally expensive, especially for large systems or long simulations. Many modelers face hardware limitations on their local machines and end up spending hours managing dependencies or queue systems on remote clusters. What if you could bypass most of that and run GROMACS simulations in the Cloud directly from your modeling platform?
The GROMACS Wizard Extension for SAMSON offers exactly this. It allows users to prepare and run molecular dynamics simulations using the GROMACS software package—either locally or in the Cloud—through a visual and interactive interface. No need to manage cluster configurations, manually upload or download files, or struggle with shell commands. Here’s how it helps:
Why Cloud Simulations Matter
Many simulation projects demand more computational resources than what’s available on a standard workstation. Whether you’re working with a large biomolecular system or need to run multiple simulations in parallel, local limitations can get in the way. Cloud computation solves that—but typically at the expense of setup complexity. The GROMACS Wizard Extension simplifies this.
One Interface, Multiple Environments
With this extension in SAMSON, you can move from system preparation to full MD simulation using GROMACS 2021.3 without leaving the platform. When you’re ready to run your simulation, just select the Cloud option—SAMSON automatically handles the upload, runs the job, and returns the results.
No scripting required, no SSH, and no job scheduler headaches. It’s ideal for users who:
- Want to take advantage of more powerful hardware accessible via the Cloud.
- Need quick iterations without constantly moving between software tools.
- Prefer a visual setup over a command-line interface.
What You Can Do in the Cloud
The Cloud integration isn’t just limited to a subset of tasks—you can carry out the full range of GROMACS workflows provided in the Wizard. This includes:
- Energy minimization
- NVT and NPT equilibration steps
- Production MD simulations
- Advanced workflows like umbrella sampling or PMF analysis
Once the job completes, results such as trajectories and plots are forwarded back to your SAMSON interface. Visualization and analysis tools in SAMSON help you immediately interpret the output.
How to Get Started
To launch computations in the Cloud with the GROMACS Wizard Extension, install it from SAMSON Connect. Once installed, you can follow the step-by-step instructions in the GROMACS Wizard tutorial under the Launching computations in the Cloud section.
You’ll be able to avoid initial software installations and jump directly from modeling to computing—hosted in the Cloud, but controlled within the same interface.
To learn more and access the full tutorial, visit the GROMACS Wizard documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.