For many molecular modelers, setting up and running simulations with GROMACS can be a time-consuming step that involves compiling complex code, managing dependencies, and tweaking performance settings for your local computer. And if you’re switching between different machines or collaborating with others, inconsistencies or installation differences can slow down progress.
What if you didn’t have to install GROMACS at all—and still run full simulations from preparation to production? The GROMACS Wizard Extension in SAMSON lets you do exactly that.
Streamlining GROMACS Simulations in the Cloud
Instead of installing GROMACS manually, the GROMACS Wizard Extension comes bundled with GROMACS 2021.3, fully integrated into SAMSON. This means you can start preparing, launching, and analyzing your molecular dynamics simulations without worrying about building the software yourself.
But more importantly, it offers built-in support to run your simulations in the Cloud—the entire pipeline—from pre-processing to production runs and output visualization. This is ideal for users who:
- Have limited local computational resources
- Need to run multiple simulations in parallel
- Want to prototype systems before scaling up
How Does It Work?
After installing the GROMACS Wizard in SAMSON, you can access Cloud mode directly from the extension’s interface. This feature appears throughout the wizard steps and allows you to switch between Local or Cloud computation modes.
In Cloud mode, your prepared simulation systems are uploaded to a cloud-services backend provided by SAMSON Connect (no need to manage clusters or VMs). Jobs are executed, and the results—simulation trajectories (.xtc), logs, and plots—are automatically retrieved back to your local session in SAMSON upon completion.
This is particularly convenient when running longer simulations such as equilibrations or production molecular dynamics, as you can continue using your local machine for other tasks while computations run asynchronously in the Cloud.
Why It Can Make a Difference
This capability is especially useful for educators, researchers, or early-stage startups who want to:
- Deliver computational training sessions without needing everyone to install GROMACS
- Maintain consistent simulation environments between collaborators
- Scale up simulations without investing in local hardware
The integration also makes it easy to visualize the results directly in SAMSON through built-in plotting and trajectory analysis features.
One-Click Deployment
To get started, all you need is:
- An installation of SAMSON
- The GROMACS Wizard Extension added via the SAMSON Connect Extension Marketplace
This setup does not require command-line expertise or administrative privileges for installation, making it one of the simplest ways to run GROMACS simulations today.
If you’ve ever spent hours configuring your environment just to run a quick simulation, this workflow could be a real time-saver.
Visit the full documentation page to explore the complete tutorial and see how to use features like batch computations, coarse-grained system setup, or custom GROMACS versions.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.