One of the most common pain points faced by molecular modelers is accessing computational power. Many molecular dynamics simulations require hundreds of thousands—or even millions—of time steps, making them time-consuming and demanding to run on personal computers. This is especially true when using powerful packages like GROMACS.
If you’ve found yourself postponing simulations or trying to optimize every nanosecond to make them run on your local machine, you’re not alone. Cloud computing can be a solution—but setting up a cloud-based environment to run GROMACS simulations usually requires complex configuration, networking knowledge, and expensive server maintenance.
That’s where the GROMACS Wizard Extension in SAMSON comes in. Designed to streamline system preparation and deployment, this extension includes a way to run simulations directly in the Cloud—without having to leave your modeling environment or set up cloud instances manually.
What Makes This Useful?
You can prepare a system, perform equilibration runs, and launch production simulations in the Cloud without writing scripts or configuring remote servers. Whether you’re testing parameters or running longer trajectories, the Cloud capability allows you to:
- Offload computationally expensive tasks from your local machine
- Avoid installing or compiling GROMACS manually
- Manage your simulations inside a graphical interface
- Receive simulation results as trajectories and plots automatically
When Should You Use Cloud Simulations?
Consider launching simulations in the Cloud when:
- Your local machine lacks memory or CPU resources
- You want to avoid long simulation times interfering with other work
- You need to run multiple simulations in parallel (batch computations are supported)
- You want to share results quickly with collaborators who don’t have local setups
How to Run GROMACS Simulations in the Cloud Using SAMSON
The process is straightforward:
- Install the GROMACS Wizard Extension via SAMSON Connect.
- Prepare your system as usual inside SAMSON (solvation, ion addition, etc.).
- Navigate to the execution step and select “Run in the Cloud.”
- Submit the job and monitor progress from the same interface.
There’s no need to manage cloud credentials or SSH keys. The integration handles the logistics, allowing you to focus on analysis and results—not infrastructure.
Beyond convenience, this approach helps reduce the friction in iterative modeling workflows. You can test hypotheses, adjust parameters, and run follow-up simulations much faster than before, especially when comparing multiple candidate systems.
To explore more about this functionality and others offered by the GROMACS Wizard—including batch computations, coarse-grained models, and protein-ligand systems—check out the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.