Running molecular dynamics (MD) simulations is a key task in computational biology, but not everyone has the local computing power to handle them efficiently—especially when dealing with complex systems or long timescales. This is where cloud computing can make a real difference. In this post, we take a close look at how SAMSON’s GROMACS Wizard makes cloud-based MD simulations more accessible and manageable, one step at a time.
If you’ve ever been limited by your local machine’s performance or if you simply want to harness the flexibility of the cloud, this walkthrough is for you. We’ll highlight the steps for launching simulations in the cloud using a simple example—the NVT Equilibration step.
Step 1: Check Before You Launch
Before pushing your simulation to the cloud, it’s recommended (though not mandatory) to try running a shorter version locally. This helps catch errors early and ensures your system is set up correctly. If your machine struggles, you can at least verify input files by using the Generate inputs button.
Step 2: Create the Job
Click the Equilibrate in the cloud or Simulate in the cloud button, based on your task. A dialog will let you select a machine type, storage size, and view cost estimates. For testing purposes, the team recommends starting with the most basic and cost-effective machine: one with 4 vCPUs and no GPU.
Step 3: Confirm and Initialize
A security dialog follows, where you can confirm the job and see the required credits. You’ll need at least one computing credit in your account to initiate any cloud job—but the actual consumption may be lower.
Once confirmed, the job appears in the Job manager window where initialization begins. Files are uploaded automatically to cloud storage, and progress indicators help track ongoing jobs.
Step 4: Start and Monitor the Job
Once initialized, you’ll be prompted to launch the job. Upon confirmation, the status will change from Starting to Running. Use the Events button to access detailed job messages and track estimated completion time.
Step 5: Download and Import Results
After completion, you’ll get a notification inside SAMSON and via email. The Job manager allows you to download all results and even helps import them back into SAMSON for further analysis and plotting.
To import results, just copy the path to your result folder and use GROMACS Wizard’s Import (*) results button. Choose the folder and confirm the files to import structures, trajectories, and generate plots seamlessly.
Tip: Don’t Forget to Clean Up
Cloud storage is convenient, but it isn’t free forever. Once you’re done, you can delete completed jobs and their files to avoid unnecessary storage costs. This can be done directly in the Job manager via the job’s context menu.
Cloud computing is a practical solution for molecular modelers facing hardware constraints or aiming to increase productivity. SAMSON’s integration of cloud computing within GROMACS Wizard ensures you don’t need to wrestle with external tools or command-line interfaces—everything happens within the same platform, with full traceability and easy access.
To learn more about launching GROMACS simulations in the Cloud using SAMSON, check out the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.