One of the most common challenges in molecular dynamics is getting simulations up and running across different computing environments. If you’ve ever struggled to compile GROMACS, wrestled with queuing systems, or managed large sets of input files on remote machines, you’re not alone. While GROMACS is a powerful package, accessing its full potential—especially in cloud or distributed settings—can be daunting.
This blog post introduces a solution to this pain point: the GROMACS Wizard Extension in SAMSON, which makes cloud-based GROMACS simulations seamless—without touching a terminal.
Why bother with cloud simulations?
High-performance computing (HPC) resources aren’t always available locally, and setting up remote simulations requires time, technical fluency, and maintenance. Cloud computing offers a flexible alternative, but many researchers don’t use it because of the overhead involved in preparing simulations, transferring files, installing dependencies, and retrieving results. With the GROMACS Wizard, these steps are fully integrated into a graphical environment—making cloud computing accessible without having to write scripts or install anything manually.
How it works
The GROMACS Wizard in SAMSON integrates cloud simulation capabilities directly into your modeling workflow. Here’s a brief look at how you can launch a simulation in the cloud:
- Prep your molecular system using the GROMACS Wizard interface.
- Select the simulation type (e.g., energy minimization, NPT equilibration, production MD).
- Click to launch the simulation in the cloud—no terminal, no manual uploads.
Once the simulation is complete, results are integrated back into your workspace. You can analyze trajectories, extract plots, and visually inspect outcomes directly in SAMSON.
Who is this useful for?
This feature is particularly helpful for:
- Researchers without access to local HPC resources.
- Students and educators who don’t want to configure complicated simulation environments.
- Molecular modelers interested in rapid prototyping and testing without committing local resources.
It also supports users who want to run batch simulations or test parameter variations efficiently, helping make research workflows more scalable and reproducible.
Local vs. Cloud: no need to choose
The GROMACS Wizard doesn’t lock you into cloud-only workflows. If you have a high-performance local build of GROMACS, you can switch the Wizard to run simulations in your environment instead. It’s flexible enough to adapt to your infrastructure, whether you’re working on a personal laptop, a university cluster, or a cloud platform.
What do you need to get started?
Just install SAMSON and add the GROMACS Wizard Extension from SAMSON Connect. Once the extension is installed, launching cloud simulations becomes a simple matter of a few clicks inside the GUI.
To learn more about launching cloud simulations using the GROMACS Wizard, visit the full tutorial documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net