Installing GROMACS for molecular modeling and simulation has traditionally been a technical barrier for many researchers and students. It often involves downloading source code, managing dependencies, ensuring compatibility with specific compilers, and sometimes taking deep dives into system-level settings. If you’re new to molecular simulations—or just want to get up and running faster—this process can quickly become overwhelming.
The GROMACS Wizard Extension in SAMSON provides a straightforward alternative: a fully integrated interface with GROMACS pre-packaged. This means you don’t have to compile or install GROMACS yourself.
Why this matters
Imagine you’re reviewing a published protein-ligand study and want to reproduce a simulation. Before you even get to the system setup, you would usually need to:
- Choose the appropriate version of GROMACS (some workflows are version-specific)
- Handle GPU or CPU optimizations
- Configure your build system if you’re compiling from source
That effort may take hours—sometimes more. And it’s not what you actually want to focus on.
The benefit of an integrated approach
By using the GROMACS Wizard Extension via the SAMSON interface, the installation becomes much simpler:
- Sign in on SAMSON Connect
- Add the GROMACS Wizard Extension
- Launch SAMSON. The extension downloads and installs automatically.
That’s it. You’re now ready to use GROMACS 2021.3 through an interface that helps you handle preparation, simulation, and results analysis—and if you prefer, you can even use your own local GROMACS installation for performance-optimized builds.
Checking your installation
Here are a few ways to check if the extension is active in SAMSON:
- Go to Home > Apps > Biology
- Check under Interface > Preferences > Updates > SAMSON Extensions
- Log in on SAMSON Connect and look in User > My Extensions
For students or researchers working across multiple systems, this cross-platform support (Windows, Linux, macOS) is especially practical. You get reproducibility and portability—without needing separate GROMACS setups for each machine.
Ultimately, this integration frees up time: you can stop fiddling with tools and start running simulations.
To learn more about the GROMACS Wizard Extension and its capabilities, including simulation workflows and advanced setup options, visit the full documentation:
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