Simplify Molecular Dynamics with Cloud Simulation in GROMACS Wizard

For molecular modelers, running complex molecular dynamics (MD) simulations often comes with a challenge: resource-heavy computations. Not everyone has access to high-performance local hardware, leading to excessive computational times or limited capabilities. However, the GROMACS Wizard in SAMSON offers a powerful solution by enabling simulations to be offloaded to cloud hardware. This feature can help you optimize resources and speed while maintaining flexibility. In this post, we’ll explore the essential steps to effectively use cloud resources for your simulations.

Why use cloud hardware for simulations?

Local hardware often struggles with larger systems or more intensive MD stages like NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation. GROMACS Wizard provides an accessible way to leverage the cloud for these heavier tasks, unlocking advanced computation capabilities without weighing down your local machine. The best part? You have full control over hardware selection, costs, and job management.

Step 1: Ensuring readiness

Before launching a job in the cloud, it’s important to set up your SAMSON environment:

  • Ensure your SAMSON Connect account has at least one computing credit. You can check this within SAMSON by going to Interface > Job manager or pressing Ctrl/Cmd + 6, and selecting the Show credits option.
  • If additional credits are needed, purchase them here.
  • Run a smaller test simulation locally to debug common errors before switching to cloud execution.

Step 2: Selecting the right machine

Choosing the appropriate cloud resources is crucial for balancing performance and costs. Here’s how:

  • Click Equilibrate in the cloud / Simulate in the cloud.
  • Use the machine-selection dialog to explore available machine types, storage sizes, and estimated costs. More details, including performance metrics, are available via the Open details button.

For testing, the tutorial suggests starting with a machine with 4 vCPUs and no GPUs, which provides a budget-friendly option. Once selected, confirm your choice to proceed.

Choose the machine type

Step 3: Submitting your job

After choosing your machine, you’ll be prompted to confirm the job submission. Here, SAMSON displays an important summary, including the estimated cost and any remaining credits in your account. You can also customize the job’s name and add notes to keep track of its context.

Once the job is confirmed, SAMSON transitions to initialization mode, where files are prepared and sent to cloud storage. Track your job’s progress using the Job manager and ensure the Running checkbox is active to display current tasks.

Job initialization

Step 4: Monitoring and downloading results

Upon job completion, SAMSON notifies you via email or within the software itself. To retrieve the results, access the job details in the Job manager, where you’ll find options to download all or specific files. The downloaded data can then be imported back into GROMACS Wizard for further analysis or visualization.

Job files

Step 5: Managing cloud storage

Once you’ve downloaded the results, it’s a good practice to delete completed jobs from cloud storage to avoid unnecessary costs. Select the job in the Job manager, right-click, and choose Delete. SAMSON ensures all data is safely removed from the cloud.

Delete a job from the list of jobs in the Job manager

Unlock the cloud's potential for your simulations

The GROMACS Wizard’s cloud computing feature transforms how molecular modelers approach simulation tasks, offering flexibility and cost management while ensuring computational workflows remain efficient. For more detailed instructions, refer to the full tutorial at this documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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