For many molecular modelers, running large-scale simulations locally can be a bottleneck in their workflow. Hardware limitations, long execution times, and system configuration issues often hinder productivity. If you’ve faced such obstacles when running GROMACS simulations, SAMSON’s GROMACS Wizard offers a streamlined solution: performing your simulations in the Cloud.
In this post, we’ll walk through how to run a molecular dynamics (MD) simulation step — specifically an NVT equilibration — in the Cloud using GROMACS Wizard in SAMSON. This approach can help you:
- Bypass local hardware restrictions.
- Access high-performance computing resources on demand.
- Stay productive while simulations run independently in the background.
Getting Ready
Before launching a Cloud job, make sure your input structure and parameters are specified. If not, follow the earlier steps related to NVT equilibration in the tutorial.
✅ You’ll also need at least 1 computing credit available in your SAMSON Connect account. You can check this in SAMSON’s Job manager or your online account.
Step-by-Step: Launching a Cloud Simulation
1. Check the System (optional but recommended)
Before launching in the cloud, try a short local run to catch any input errors. Alternatively, click “Generate inputs” to validate files.
2. Create the Job
Click Equilibrate in the cloud. In the dialog that appears, choose your machine type, including CPU count and storage size. Viewing performance and pricing details helps tailor the job to your needs.
3. Confirm and Launch
A security prompt shows job details and ensures computing credits are available. Click OK to submit.
4. Monitor via Job Manager
Job initialization uploads files to Cloud storage. Use the Job manager to monitor progress and view logs. The interface clearly shows job status triggers — from Initializing to Running.
5. Completion & File Retrieval
Once completed, you’ll receive a notification. Return to the Job manager, right-click your job, and choose Open result window to download results files.
We recommend clicking Download all to ensure you retrieve everything necessary for post-processing.
6. Import into GROMACS Wizard
After downloading, import the results back into the GROMACS Wizard using the Import (*) results button in the appropriate tab. Paste the previously copied path, then review and import simulation trajectories and plots.
7. Wrap Up and Clean Up
If you no longer need to store results in the Cloud, delete the job to avoid future storage deductions from your credits. Jobs can be deleted directly from the Job manager with a right-click.
Why Run in the Cloud?
Cloud simulations are ideal when:
- Your machine can’t handle the system complexity.
- You want to run simulations in parallel with other work.
- You need access to scalable resources temporarily.
The GROMACS Wizard makes Cloud execution approachable through guided dialogs and a transparent credit system. You stay in control — from setup to final file retrieval — while offloading computation elsewhere.
To learn more about running GROMACS computations in the Cloud with SAMSON, visit the original documentation page:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.