Running molecular dynamics (MD) simulations can be time-consuming and resource-intensive. Many researchers find themselves waiting on local machines for hours — if not days — for simulations to finish. Upgrading local hardware is not always an option, and institutional clusters often have long queues. If this sounds familiar, you’re not alone.
The GROMACS Wizard Extension for SAMSON offers a practical solution: launching MD computations directly in the Cloud, without leaving the interface. This feature makes high-performance simulations accessible without needing to configure a remote server or install GROMACS separately.
Who is this for?
This feature is especially useful for:
- Researchers who don’t have access to powerful local computing infrastructure.
- Students and academic users running complex or long simulations.
- Anyone who wants to test multiple parameters without tying up their main machine.
How it works
The GROMACS Wizard ships with support for both local and cloud-based simulation. When you prepare a system in the GROMACS Wizard interface — setting up your periodic systems, running energy minimization, equilibration, and defining production runs — you have the option to execute the simulation remotely.
This eliminates common pain points such as:
- Having to compile or install GROMACS and dependencies on a remote server.
- Transferring molecular setup files between machines.
- Monitoring complex simulations remotely via command-line tools.
Instead, the process is integrated into SAMSON: once your system is ready, choose the Cloud option to run the simulation. The wizard handles the remote launch and brings back the results — including the trajectories and plots — directly into your workspace.
Why does this matter?
Cloud computing allows researchers to offload simulations and keep working or analyzing other data without interruptions — even from a laptop. This hybrid flexibility (local + cloud) is especially helpful when dealing with large biomolecular systems or testing several parameter sets in parallel (as is often the case in free energy calculations or umbrella sampling).
What’s needed to get started
First, install the GROMACS Wizard Extension via the SAMSON Connect platform. Once installed and active in SAMSON, prepare your system as usual and select the Cloud option when launching the computation.
If you’d like step-by-step guidance, the Cloud computing section of the tutorial provides all the practical details.
Wrapping up
The ability to launch GROMACS simulations in the Cloud can save time and open modeling capabilities to users who otherwise wouldn’t have sufficient local computational resources. Whether you’re an academic researcher or simply experimenting with MD for the first time, this feature helps streamline your workflow and focus more on science than setup.
To learn more and explore the full tutorial, visit the GROMACS Wizard Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.