Molecular dynamics (MD) simulations can be time-consuming, especially when you’re working with larger systems or limited local computational power. For many molecular modelers, long simulations mean one thing: your workstation becomes unusable for hours, or even days. Luckily, SAMSON GROMACS Wizard offers a convenient alternative—running MD simulations in the cloud.
Whether you’re running NVT Equilibration, NPT Equilibration, or full Production MD, you can offload the heavy lifting to the cloud with just a few clicks, freeing up your machine and your time. Here’s how the workflow looks and how it can help you.
Why Run in the Cloud?
- Work on other tasks while simulations run in the background
- Choose computational resources to fit your needs and budget
- No file transfer fees, even when downloading large result files
All you need is at least 1 computing credit (you can check and purchase credits on SAMSON Connect).
Step-by-step Cloud Workflow
1. Choose Your Machine
After defining your simulation parameters, click Equilibrate in the cloud / Simulate in the cloud. A dialog lets you pick machine specs and storage size along with cost estimates. For short test jobs, a 4 vCPU / no GPU machine is a cost-effective choice:
2. Confirm Submission
A confirmation dialog summarizes the job details and required credits. You’re also free to rename the job or add notes. This step helps avoid accidental charges and lets you stay organized.
3. Monitor Progress
Once submitted, the Job manager handles the rest: packaging inputs, uploading them, and initializing the job. When the system is ready, you’ll get a prompt to start your simulation.
4. Relax (or Keep Working)
While your simulation runs in the cloud, you can continue working on other parts of your project—or even shut down SAMSON entirely. Results stay in your cloud storage, and when the job is done, you’ll be notified via email and in the SAMSON News tab.
5. Download and Analyze
Use the Job manager to view and download results. A dedicated file browser lets you choose individual or all result files. For most workflows, downloading all files is recommended so that nothing is missing for post-processing.
6. Import Results
Back in GROMACS Wizard, simply paste the result folder path and import results for analysis and visualization. Dialogs will guide you through trajectory imports and generate plots automatically.
Final Tip: Clean Up When You’re Done
Even though storage costs are minimal, it’s a good habit to delete jobs you no longer need. Via the Job manager, right-click a completed job and select Delete to remove it from the cloud and stop incurring storage charges.
Cloud-based simulations are not just for scaling up—sometimes they’re just the right way to stay productive while your molecules do their thing in silico.
To learn more, explore the complete documentation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.