Running molecular dynamics simulations often requires significant computational resources — the kind most laptops or even desktops can’t provide for large or long simulations. For many molecular modelers, this turns an exciting project into a frustrating wait. One elegant solution is cloud computing, and with the GROMACS Wizard in SAMSON, launching GROMACS jobs in the cloud is easier than ever — and faster than you might expect.
This post focuses on how you can run an NVT Equilibration simulation in the cloud using the GROMACS Wizard in SAMSON. The same process applies to NPT Equilibration and production MD. If you’ve ever been held back by limited hardware, this will likely change your workflow.
🧠 The Problem: Local Limits
Many molecular systems you might want to simulate are simply too large for typical machines to handle efficiently. Even if local computation works for small systems, larger ones lead to long delays or failed runs. And testing your system configuration locally might still not give you confidence that the full simulation will proceed smoothly.
🔗 The Solution: Delegating to the Cloud
With SAMSON’s GROMACS Wizard, you can easily launch cloud-based simulations. Simply prepare your simulation parameters as usual, confirm you have at least 1 computing credit in your SAMSON Connect account, and then:
- Create the job via the “Equilibrate/Simulate in the cloud” button.
- Select your compute machine and storage options. You can view machine characteristics and pricing depending on your needs.
- Confirm the job in a secure dialog that shows job details, including estimated costs.
- Initialize the job. SAMSON prepares the job files and uploads them to the cloud.
🚀 Starting and Monitoring
After initialization, you’ll get prompted to start the job. Once running, you can monitor it through the Job Manager, which shows progress, job events, estimated completion time, and more. Crucially, you can even close SAMSON while the computation proceeds in the background — a freedom local runs rarely offer.
📥 Downloading and Using Results
After the simulation finishes, you’ll receive an automatic notification and can download results using the Job Files window. We recommend downloading all files, since they’re useful for post-processing or extending the simulation.
You can then re-import the data directly into the GROMACS Wizard for analysis or for use in the next simulation step.
🧹 Tidying Up
Finished? You can delete the job from the cloud to save computing credits by avoiding ongoing storage costs. Don’t worry — SAMSON will prompt you to confirm before any deletion.
✨ Why Modelers Appreciate It
Beyond the hardware savings and improved scalability, cloud computations simplify job management and free your local machine for other tasks. You can easily pause, cancel, or review jobs from your dashboard. For exploratory modeling or iterative workflows, that freedom is hugely empowering.
To learn more about launching GROMACS computations in the cloud using SAMSON, visit 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 get SAMSON here.