If you’ve ever run molecular dynamics simulations with GROMACS, you already know how demanding they can be in terms of computational resources. Long trajectories, multiple replicas, and fine-grained time steps can push even powerful workstations to their limits. But what if you could shift the heavy lifting to the cloud—without needing to script job submissions or configure remote servers yourself?
The GROMACS Wizard Extension for SAMSON makes cloud-based simulation surprisingly accessible, even for those with little or no experience in high-performance computing environments. It provides an interface to run full GROMACS workflows locally or in the cloud, and can be especially useful when your local machine isn’t fit for intensive simulations or you want to run multiple simulations in parallel.
What pain does this solve?
Running simulations on personal machines can be frustrating due to limited CPU or GPU resources. Even if you compile an optimized version of GROMACS for your hardware, your system may become unresponsive or prevent you from doing other work during large simulation runs. And while cloud platforms promise scalability, configuring clusters and writing job submission scripts can be overwhelming.
The cloud execution feature of GROMACS Wizard addresses this by providing a painless setup that integrates directly into the SAMSON interface. You don’t need to leave the platform or configure anything manually. As long as you’re signed into your SAMSON Connect account, launching cloud simulations becomes a matter of a few clicks.
How does it work?
After preparing your system using the steps in the GROMACS Wizard (such as energy minimization and equilibration), you can move to the final production simulation step. Here, the wizard gives you the option to launch your computation in the cloud instead of locally. The extension will handle:
- Packaging all input files;
- Transferring them to the compute environment;
- Launching the simulation on remote machines powered by hardware suitable for molecular dynamics;
- Retrieving results upon completion.
The process is secure, and progress can be monitored directly within SAMSON. When the jobs finish, your simulation trajectories and energy plots are downloaded and visualized as if they’d been run locally.
When should you use this?
You might consider cloud simulation if:
- Your local hardware isn’t sufficient for long or complex simulations.
- You need to run many simulations in batch (parameter sweeps, replica exchange, etc.).
- You want to continue working on your computer without interruptions from heavy computations.
- You don’t have access to in-house HPC resources but need scalable computation.
Even if you prefer running small test systems locally, using the cloud becomes invaluable when scaling up or sharing computing resources with a team.
Getting started
You’ll find the option for cloud simulation in the wizard’s later steps—particularly during the production molecular dynamics stage. You can enable this in just a few clicks.
For a step-by-step guide, including screenshots and setup help, visit the original tutorial page here: GROMACS Wizard – SAMSON Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.