Running molecular dynamics (MD) simulations, especially on large biomolecular systems, often pushes the limits of a researcher’s local hardware. If you’ve ever faced crashes due to memory overload or critical slowdowns on NVT or NPT equilibrations, you’re not alone. This is a common pain for molecular modelers.
Fortunately, SAMSON’s GROMACS Wizard offers an integrated solution: launching simulations in the cloud, without leaving your familiar interface — and without needing to manage remote servers or write scripts.
Why consider the cloud?
Even short MD simulations can quickly become demanding in terms of memory and CPU. When your laptop freezes or your job fails after long setup times, the frustration is real. Running in the cloud offers:
- Scalability: Choose machines with more vCPUs or even GPU support.
- Accessibility: No need to install or configure cluster software.
- Integration: Everything is handled within the SAMSON interface, using the Job manager.
How it works in SAMSON
Once your system is prepared and parameters are set for a simulation step such as NVT Equilibration, cloud submission becomes straightforward:
1. Choosing a machine
Click on Equilibrate in the cloud (or Simulate in the cloud, depending on the step), then choose your desired machine type, storage size, and see associated costs.
2. Confirming your job
Before launching, a dialog lets you review the machine’s configuration and confirm. It also makes it clear how many computing credits will be used (only machine and storage usage are billed — file transfers are free).
3. Monitoring progress
SAMSON’s Job manager lets you track initialization, starting, and running phases. You can also see estimated completion time from GROMACS, and view messages and logs throughout the job’s life.
4. Closing SAMSON? No problem
Jobs continue running in the cloud independently. Even if you close SAMSON, the results will be waiting when you return. Perfect for running overnight tasks or avoiding local bottlenecks.
5. Downloading and importing results
Once completed, you’ll receive a notification. From the Job manager, download all result files with one click.
Then, import the results directly into the GROMACS Wizard, analyze your trajectories, generate plots, and continue your workflow, all inside SAMSON.
Focus on modeling, not infrastructure
With cloud computation, you no longer need to worry about hardware limitations or setting up remote services. Whether you’re testing a model or running production-level simulations, the process stays the same and lives entirely within your modeling environment.
To learn more about performing GROMACS computations in the cloud using SAMSON, visit the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.