Molecular modelers and simulation scientists often run into the same frustrating bottleneck: long simulation wait times and resource limits on their local machines. Whether it’s for NVT/NPT equilibration or production molecular dynamics runs, the hardware constraint often becomes the biggest roadblock in your workflow.
If you’re using the GROMACS Wizard in SAMSON, you may not realize there’s a powerful solution already built in: you can run simulations in the Cloud with just a few clicks.
Minimize Setup Time, Maximize Efficiency
Instead of wrestling with cluster job schedulers or navigating complex command-line setups, the GROMACS Wizard walks you through a dead-simple process to launch a Cloud-based simulation. If you’ve already configured your input structure and parameters, starting a Cloud run is literally a matter of choosing a machine, confirming, and watching the magic happen.
Choose the Machine That Fits Your Test
Not all simulations need expensive high-performance GPUs. For test runs and light workloads, you can select a machine with 4 vCPUs and no GPU, which is the most affordable option. The interface shows pricing hints so you can balance cost and performance gradually as you scale.
From Confirmation to Initialization
After selecting a setup, SAMSON gives you a job summary before launching the computation. This includes the estimated cost in computing credits, which are lightweight units you can acquire in your SAMSON Connect account. You only need 1 credit in your account to initiate a Cloud job—often, jobs will use even less.
Monitoring Progress (Even If You Close SAMSON)
Once the job is started, the Job manager lets you observe everything in real-time: from status updates to logs. You can safely minimize or fully close SAMSON while the job continues in background Cloud service.
And you’ll get an email notification (plus a SAMSON news alert) once the job is completed, so you can jump back in exactly when needed.
Download and Import with a Few Clicks
Retrieving your results is just as straightforward. Use the context menu in the Job manager to download all result files. Once saved locally, import them directly into GROMACS Wizard to generate trajectory plots or continue into the next simulation step.
Whether you’re jumping into the next production stage or analyzing data, the transition from Cloud results to local workspace is designed to be smooth.
Why Use the Cloud for GROMACS?
- Run simulations without local hardware limitations
- Test setups before fully committing to long simulations
- Access simulation data anytime, even from another location
- Avoid complex HPC setup and maintenance
This feature won’t replace local simulations for every case, but it can serve as an efficient supplement—especially when working with large systems or when traveling without access to your usual machine.
To learn more about Cloud simulations using GROMACS in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.