For many molecular modelers, installing and configuring GROMACS — especially with specific compiler flags, MPI settings, or GPU configurations — is a significant hurdle. It can take hours or even days to get everything working properly and reproducibly across different machines. What if you could skip all that completely?
The GROMACS Wizard Extension for SAMSON offers exactly that: a pre-configured, ready-to-use integration of GROMACS within a visual molecular design environment. There’s no need for manual compilation, dependency handling, or environment configuration. Instead, you install the extension, launch SAMSON, and it’s ready to go — on Windows, Linux, and MacOS.
What’s included?
The GROMACS Wizard Extension ships with GROMACS 2021.3, so all the core functionality of GROMACS is already embedded. That means:
- Pre-processing and system preparation tools
- Energy minimization and NVT/NPT equilibration
- Production molecular dynamics (MD) simulation features
- Access to pre- and post-processing utilities
- A visual interface integrated into SAMSON
What if you already have GROMACS installed?
If you’ve already built and optimized your own installation of GROMACS — for example, compiled with CUDA and OpenMPI for high-performance clusters — the extension lets you keep using it. You can select your own local GROMACS installation and run simulations directly from SAMSON through an intuitive interface.
Making life easier for newcomers
Suppose you’re new to molecular dynamics and still trying to navigate the command-line interface of GROMACS. The GROMACS Wizard acts as a visual guide that walks you through each simulation step, with interface widgets to select options and parameters. You don’t have to remember complicated command syntax or keep switching between a terminal and a text editor.
How to install it?
1. Sign in at SAMSON Connect and go to the Extensions page
2. Find the GROMACS Wizard Extension and click to add it to your setup
3. Launch SAMSON, and the extension will automatically download and install
You can verify that it’s installed through several routes:
- Under Home > Apps > Biology within SAMSON
- In Interface > Preferences > Updates > SAMSON Extensions
- In User > My Extensions on the SAMSON Connect website
This approach frees researchers, educators, and students from spending valuable time on software setup and lets them focus directly on model building and simulations.
To learn more, visit the full tutorial page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.