If you’ve ever tried to simulate a large molecular system using GROMACS, you’ve probably run into limitations on your local machine. RAM usage, simulation time, or even GPU availability can quickly become bottlenecks.
Fortunately, the GROMACS Wizard extension in SAMSON gives molecular modelers an alternative: smooth integration with Cloud resources, right inside the platform. This is a game-changer for those who don’t have access to local high-performance clusters or want to test simulations without affecting their personal computer’s performance.
What Makes Cloud GROMACS Different?
Instead of configuring remote servers or manually uploading input files, SAMSON’s GROMACS Wizard handles cloud-based simulation workflows with a few clicks. Whether you’re doing equilibrations or production simulations, your job runs on managed compute nodes with transparent pricing and simple storage options. 🧪☁️
Step-by-Step: Submitting a Cloud Job
Here’s a brief tour of how it works when launching an NVT Equilibration job (NPT and Production MD follow the same steps):
- Generate inputs if you’re unable to run locally. This step checks for basic sanity in your system.
- Click Equilibrate in the cloud. You’ll be prompted to select a machine type.
- Review machine details (vCPUs, storage, pricing) and click OK. It’s suggested to start with a 4 vCPU machine without GPU for test runs.
- A confirmation dialog will appear showing how many credits you’ll use. Confirm to continue.
- Job initialization begins—files are prepared and uploaded.
- Once ready, you’ll be asked to confirm the start of the simulation.
Monitoring Without the Stress
SAMSON’s built-in Job manager lets you track job status, view logs, and check estimated completion times. When a job is complete, you’ll receive a notification and can easily download the results directly from the interface.
Even better—simulations run independently of your machine. You’re free to continue working in SAMSON or even close it entirely while jobs progress on the Cloud.
Still Have Control
Need to cancel or pause a running job? You can. Want to re-import results to visualize trajectories or tweak analysis? Also possible. Once you’re done with the files, you can delete the job to save storage credits.
Who Benefits Most?
This cloud-based approach is particularly helpful for:
- Researchers without compute clusters
- Students who want to quickly validate a model
- Molecular modelers exploring large systems
- Collaborators working on shared cloud resources
To learn more about configuring, running, and managing cloud-based GROMACS simulations with SAMSON, check out the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.