For many molecular modelers, the challenge of running large-scale simulations often starts after system preparation. While GROMACS is a powerful molecular dynamics package, deploying simulations on the cloud or HPC infrastructure can be time-consuming and complex—especially for users without experience configuring remote environments.
The GROMACS Wizard Extension in SAMSON addresses this pain directly by making it possible to launch GROMACS simulations in the cloud directly from its graphical interface. No terminal commands, no SSH — just a few clicks.
Why run in the Cloud?
Cloud-based simulations allow you to:
- Run computations that exceed your local hardware capacity
- Avoid long computation times on personal devices
- Keep your workstation available while intensive tasks run elsewhere
For researchers and students dealing with models that require extensive system size, long timescales or multiple trajectories (like umbrella sampling or protein-ligand stability simulations), cloud computing can significantly speed up your workflow without needing your own cluster.
How does it work in SAMSON?
Thanks to the GROMACS Wizard Extension in SAMSON, you can launch cloud simulations without configuring remote clusters yourself. You simply prepare your system using the extension’s built-in steps (from energy minimization to equilibration), and then use the provided interface to run the simulation in the cloud.
The extension integrates this feature seamlessly, ensuring that everything from pre-processing to result retrieval is managed from within SAMSON. Once the cloud job completes, you download trajectories and analyze them using SAMSON’s visualization tools or continue processing with GROMACS commands.
A typical workflow
Here’s what a typical cloud-based simulation flow looks like in SAMSON:
- Prepare your system (structure, solvation, ions, topology)
- Minimize energy
- Run NVT + NPT equilibration
- Run production MD
- Launch the production run in the Cloud directly from the interface
- Retrieve and analyze results in SAMSON
This is especially helpful when you’re working with long production runs or performing parameter sweeps and batch simulations that would otherwise tie up your local computer for hours (or days).
No compilation required
The extension ships with GROMACS pre-installed (GROMACS 2021.3), so there’s no complicated build process. However, power users who want to use custom builds or a local GROMACS installation can still configure the extension to use those instead.
Cross-platform support
The GROMACS Wizard Extension supports Windows, Linux, and macOS. So you can offload computations regardless of your operating system.
To explore the full tutorial and see how to launch computations in the cloud within SAMSON, visit the original documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.