One common challenge for molecular modelers is performing large-scale or lengthy GROMACS simulations without overloading their local machines. Interactive work becomes sluggish, fans spin up, and background simulations may suddenly halt if the system goes idle or reboots. What if your simulation could run smoothly in the background—remotely—without occupying your own system?
This is where the GROMACS Wizard Extension for SAMSON offers a very practical solution: with built-in support for cloud-based computation, it helps you launch simulations directly in the cloud from your SAMSON workspace, freeing up your system for other tasks. Whether you’re running energy minimization or production MD on complex systems, the cloud support removes the need for dedicated workstations or complex SSH scripts.
How it works
Once you have prepared your system in SAMSON using the GROMACS Wizard interface, launching your simulation in the cloud is only a few clicks away. In the tutorial, you’ll find a step-by-step guide for each stage: from pre-processing structures to launching energy minimization and dynamics runs remotely.
Let’s walk through a typical workflow:
- Prepare your system locally using the Prepare step provided in the GROMACS Wizard.
- Perform optional local runs such as energy minimization to verify initial setup.
- When ready, navigate to the Cloud section of the Wizard to launch your simulations in the cloud.
- Configure resource parameters if necessary (for example, number of cores, duration or GROMACS binary version).
- Monitor the progress and retrieve simulation results such as trajectories and energy plots once they complete.
All this is integrated directly into the SAMSON interface, removing the need to learn cloud storage or job scheduling tools separately. The system can even use your own precompiled version of GROMACS for higher performance compatibility.
Why it helps
For users working on molecular dynamics projects with large systems—like membrane proteins or lengthy sampling schemes (e.g., umbrella sampling or COM pulling)—this cloud capability is not just about performance, but reliability and flexibility.
Students working on laptops no longer need to keep improvised servers running overnight. Researchers with limited workstation access can test multiple setups in parallel. And teams can easily reproduce simulations across shared cloud setups with minimum manual configuration.
If you’re frequently managing long GROMACS jobs and wish your computer could stay cool and responsive during lunch breaks, the cloud support in SAMSON’s GROMACS Wizard might be what you’re looking for.
To explore this in more detail, and access the full guide including screenshots and usage examples, visit the GROMACS Wizard tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.