Preparing and running molecular dynamics simulations can be time-consuming and resource-intensive, especially when working with large or complex systems. One common challenge for molecular modelers is limited access to high-performance computing resources, which are often required for extensive GROMACS simulations. Waiting hours—sometimes days—for results on local machines is not uncommon, especially when multiple simulations need to be queued or run in series.
If you’re using GROMACS through SAMSON, there’s a built-in way to move beyond local CPU constraints: running GROMACS simulations directly in the Cloud using the GROMACS Wizard Extension.
Why Cloud Simulations?
- Offload heavy computations: Run simulations without tying up your local machine.
- Parallelize tasks: Launch multiple jobs at once in the Cloud to explore parameter spaces or series of systems.
- Stay platform-agnostic: Whether you’re on Windows, Linux, or macOS, Cloud computation offers consistent performance.
How to Launch a GROMACS Simulation in the Cloud Using SAMSON
Once you’ve installed the GROMACS Wizard Extension in SAMSON, launching computations in the Cloud is straightforward. Here’s a step-by-step outline of the process:
- Prepare your system as usual using the step-by-step workflow provided by the extension (from topology generation to equilibration).
- Go to the final step — Production Molecular Dynamics Simulation.
- In the production simulation settings, you’ll find an option to choose the
Execution Platform. Select Cloud. - SAMSON will automatically handle packaging your input files and uploading them to the SAMSON Cloud infrastructure.
- You’ll receive progress updates directly within the SAMSON interface, and when the job is finished, trajectory and analysis data will be downloadable right into your session.
When Should You Use the Cloud Option?
Cloud simulations are particularly useful when:
- You deal with long timescales or large biomolecular systems.
- You need results quickly and want to avoid local queueing or system limitations.
- Your local system lacks a high-performance build of GROMACS optimized for your specific CPU/GPU.
Tips for Efficient Cloud Usage
- Test locally first: Run a short simulation locally to ensure your system is well-prepared before launching the full version in the Cloud.
- Tune simulation length: Start with shorter production runs to estimate costs and runtime before scaling up.
- Use batch computations: Combine Cloud execution with batch job functionality in GROMACS Wizard for systematic simulations — such as free energy calculations or ligand scans.
If you’re new to this or want to explore further options—like combining it with umbrella sampling or PMF studies—you can consult the full tutorial available in the documentation.
Cloud simulations offer a way to scale your work without investing in new hardware or complex infrastructure. If you’re already using SAMSON, this approach integrates seamlessly into your workflow.
To learn more, visit the full GROMACS Wizard tutorial at https://documentation.samson-connect.net/tutorials/gromacs-wizard/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.