Running molecular dynamics (MD) simulations can often be a resource-intensive task. For molecular modelers working on large systems or simulations that need to run for extended periods of time, local computational resources quickly become a bottleneck. But what if launching GROMACS jobs in the cloud was just a few clicks away—directly within your modeling platform?
If you’re using the GROMACS Wizard inside SAMSON, cloud computing isn’t just accessible—it’s seamless. In this post, we’ll walk through how you can launch a cloud-based GROMACS simulation from inside SAMSON, monitor job progress, and download results efficiently. Whether you’re doing NVT equilibration, NPT equilibration, or a production MD simulation, the process is the same.
Why run GROMACS in the cloud?
Some real-life reasons:
- Your laptop isn’t powerful enough to simulate the system.
- You want to multitask while simulations run elsewhere.
- You’re trying to keep your local machine available for other tasks.
Step-by-step: Launching a GROMACS Job in the Cloud
1. Get your credits 💳
Before you start, make sure you have at least 1 computing credit in your SAMSON Connect account. You can check this inside SAMSON’s Job manager (Ctrl/Cmd + 6), or on SAMSON Connect itself.
2. Choose your machine
Click the Equilibrate in the cloud or Simulate in the cloud button. A dialog will appear, allowing you to choose VM specs (like number of CPUs, storage size, and cost). For testing or small simulations, the 4 vCPUs and no GPU option is the most cost-effective.
3. Confirm and submit
A confirmation dialog will summarize your configuration, including your available credits and job cost estimate. You can also rename the job and add notes before submitting.
4. Track job progress
After submission, the Job manager will show the job’s status—from initial upload, to starting, to running. You can open the job details to view logs, cost, events, and more.
5. Wait or walk away
You don’t have to keep SAMSON open. Cloud jobs continue running in the background. When done, you’ll receive a notification and be able to download the results later.
6. Download and analyze 📦
Once complete, open the job context menu and choose Open result window. You can download individual files or use Download all to fetch everything needed for post-processing.
7. Import into GROMACS Wizard
Use the Import results button from the relevant simulation tab (e.g. Equilibrate – NVT) to load your files into SAMSON. You’ll be able to visualize trajectories or generate relevant plots in just a few seconds.
Wrap-up: Clean as you go
If you no longer need the results stored in the cloud, you can delete the job via the Job manager. This helps prevent unnecessary storage charges from eating into your credits.
Cloud computing allows you to stay productive while your simulations run somewhere else, and SAMSON’s tight integration makes it easy to set up and manage jobs without ever needing to leave the platform.
To dive deeper into cloud computing with GROMACS Wizard in SAMSON, see the full documentation page here: 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.