Molecular simulations can be computationally intensive. Running extensive molecular dynamics (MD) simulations with GROMACS often requires significant local hardware resources, time, and configuration. This becomes a common bottleneck for researchers and students alike who need results but lack high-performance machines or time for setup.
If this sounds familiar, you might want to explore running your GROMACS simulations in the cloud—directly from SAMSON, thanks to its GROMACS Wizard Extension.
Why consider cloud simulations?
Cloud computing offers flexibility: run demanding simulations without being limited by your local machine’s capacity. You can keep working on other tasks while the computation happens remotely and receive results once finished. This is especially useful during training, coursework deadlines, or to avoid clashing with other computationally heavy tasks occurring locally.
How it works in SAMSON
The GROMACS Wizard Extension for SAMSON integrates a complete workflow for GROMACS simulations—including pre-processing, energy minimization, equilibration, and production runs—and includes the ability to launch these simulations in the Cloud.
From within the familiar SAMSON interface, you can:
- Prepare your system using a step-by-step interface.
- Easily switch from local to cloud computation.
- Submit jobs to the cloud without configuring a remote server yourself.
- Retrieve results as trajectory files and visualization plots once your simulation is finished.
No extra installation is required: the extension ships with GROMACS (currently version 2021.3), and installation instructions are minimal—thanks to SAMSON’s one-click extension system.
When should you use the Cloud?
Consider running simulations in the Cloud when:
- Your local machine lacks sufficient CPU/GPU power or memory.
- You have multiple simulations to run in parallel (e.g., umbrella sampling, coarse-grained tests).
- You want to offload simulations and continue working without slowing your laptop down.
- You’re collaborating with others and want a reproducible and centralized setup for running simulations.
Getting started
To try this out, install the GROMACS Wizard Extension via SAMSON Connect. Once added, you will find cloud computation features integrated in the workflow after system preparation stages. If you don’t see it, check under Home > Apps > Biology.
This setup is cross-platform and available on Windows, Linux, and macOS. And the best part? You don’t need to configure GROMACS installations yourself. Still want to use a custom build of GROMACS that you optimized? SAMSON supports that too.
Cloud-based simulations from SAMSON make molecular modeling much more accessible and scalable—no matter the power of your local setup. That’s one less technical barrier in your way.
Want to dig deeper and try this for your own system? Visit the full tutorial for step-by-step instructions on launching cloud-based GROMACS simulations: SAMSON GROMACS Wizard Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.