Preparing and running molecular dynamics (MD) simulations locally often requires significant setup: installing packages, managing dependencies, compiling code, setting up GPUs and CPUs, and more. For many molecular modelers, this overhead is frustrating—especially when it takes more time to set up a simulation than to analyze its results.
What if you could skip all that, and run GROMACS simulations directly in the Cloud from your modeling interface—no manual node configuration, and no installation of GROMACS required? This is where the GROMACS Wizard Extension for SAMSON comes in. It lets you send simulations directly to the Cloud, straight from your molecular modeling environment.
The GROMACS Wizard Extension integrates GROMACS (version 2021.3) into SAMSON and provides a streamlined interface to prepare, run, and retrieve results from Cloud-based simulations. Here’s what you gain by using it:
Why Use Cloud Simulations?
Even with good local resources, some simulations are simply too large or time-sensitive to run on personal machines. With the GROMACS Wizard Extension, you can:
- Bypass the hassle of installing or compiling GROMACS yourself
- Launch simulations in the Cloud from within the SAMSON interface
- Retrieve simulation trajectories and plots directly for analysis
Everything, including system preparation, energy minimization, and setting up equilibration steps, can be done interactively. Think of it as having access to a fully-configured remote cluster, without ever opening a separate terminal.
How It Works
Once you install the GROMACS Wizard Extension from SAMSON Connect, you’ll be able to prepare your system in a few intuitive steps. When it’s time to run your simulation, you simply choose to launch it in the Cloud.
Here’s an outline of the workflow:
- Build or load your system in SAMSON
- Use the GROMACS Wizard to preprocess and prepare your system
- Select the simulation step (e.g. NVT, NPT, full MD)
- Choose “Run in the Cloud” to launch your simulation remotely
- Analyze the results — trajectories, energy plots, and more
The process is especially valuable for users dealing with multiple systems or high-throughput calculations, where local resources become a bottleneck.
What You Need to Get Started
To try Cloud-based simulations, you need to:
- Install SAMSON, available on SAMSON Connect
- Add the GROMACS Wizard Extension via the Extensions menu
- Launch SAMSON and access the Wizard from Home > Apps > Biology
Once set up, the Cloud option is available in the simulation steps menu. No further configuration is necessary—the system automatically handles the execution remotely.
Benefits in a Nutshell
- Save time and avoid installation hassles
- No GROMACS compiling or dependency management
- Run large simulations without overloading your local machine
- Access results (e.g., trajectories and energy plots) fast
Want to try it out or learn more? Check out the detailed documentation on Cloud simulations here: GROMACS Wizard – Launching computations in the Cloud.
Learn more in the full GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.