Running molecular dynamics simulations can be resource-intensive. If you’ve ever started a GROMACS job only to watch your workstation crawl to a halt—or worse, crash—you’re not alone. For many researchers and students, limited computing power can be a major bottleneck when it comes to analyzing large biomolecular systems or running long simulations.
Fortunately, if you’re using the SAMSON platform, there’s a built-in solution: the GROMACS Wizard Extension lets you run your simulations not only locally, but also in the cloud. This means you can keep designing, analyzing, or even just using your computer for other tasks while your simulations run remotely.
Why move to the cloud?
Cloud-based simulations offer several advantages for molecular modelers:
- Save computing power: Offloading simulations lets your machine stay responsive.
- Handle larger systems: Cloud nodes can be configured with powerful CPUs or GPUs.
- Run multiple jobs simultaneously: Perfect for batch processing or scanning parameter sets.
- Remote monitoring: You can launch jobs and check on them later from any system with SAMSON installed.
How cloud simulations work in the GROMACS Wizard
When using the GROMACS Wizard Extension in SAMSON, you have the option to launch your computations in the cloud. The wizard provides a straightforward interface to set up your system, define simulation parameters, and submit the job to a cloud provider directly from the SAMSON interface. The main steps are:
- Prepare your system locally using standard GROMACS steps embedded in the wizard (e.g., preprocessing, energy minimization, equilibration stages).
- Click on the cloud computing option in the wizard interface.
- Define how the job should be run in the cloud: system size, duration of simulation, performance parameters, etc.
- Submit your job and let the cloud handle the computational burden.
This cloud feature is particularly handy for simulations that would take hours or days on local machines. It also enables users without access to institutional clusters to still run valuable calculations.
Use cases
This workflow is useful in multiple contexts:
- Teaching environments: Instructors can guide students through real GROMACS simulations without needing every student to have a strong computer.
- Early-stage modeling: You can test different configurations without committing large portions of local resources.
- Field work: If you’re traveling with a lightweight laptop, the simulation doesn’t have to wait.
For many, the shift to cloud-based simulation offers a much-needed balance between performance and flexibility.
The GROMACS Wizard Extension also lets you specify a custom version of GROMACS or performance parameters depending on your project’s requirements. Whether you’re just getting started or have highly customized workflows, you can tailor the setup to your needs.
To learn more about running GROMACS simulations in the cloud with the SAMSON GROMACS Wizard, visit the full documentation 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.