Running molecular dynamics (MD) simulations often involves long preparation steps, software installation and compilation, and configuration of local computing resources. If you’re working in a constrained environment (e.g., a classroom, a shared lab PC, or just traveling with a lightweight laptop), these barriers can delay your research or teaching. Fortunately, SAMSON’s GROMACS Wizard Extension offers the option to perform your full GROMACS workflow — in the Cloud.
Imagine this: you’re preparing molecular systems, tweaking force field parameters, generating index groups, and analyzing free energy — and you don’t need to worry about whether GROMACS is properly compiled on your specific system. The GROMACS Wizard packs all of that in one integrated solution that runs locally or in the Cloud when you want it to. Here’s how it works and how it helps.
The problem: Installation and hardware limitations
GROMACS is a powerful tool for molecular simulations, but not always easy to set up. Compiling GROMACS from source, configuring the right libraries (MPI, FFT, CUDA if you’re using GPUs), and ensuring compatibility with your operating system — these are repetitive steps that take time and sometimes lead to frustration.
Even when everything is correctly installed, you might find yourself limited by your hardware. Running a simulation with thousands of atoms on a laptop may take hours or days, and using institutional HPC resources involves long queues or complex submission systems.
The solution: Launching simulations in the Cloud with GROMACS Wizard
With the GROMACS Wizard Extension in SAMSON, you can prepare your system as usual with an intuitive graphical interface, and when you’re ready to run your simulation, simply choose to launch it in the Cloud.
There’s no need to install GROMACS — the extension includes a recent version (currently GROMACS 2021.3), and it’s ready to use immediately. If you want, you can configure the Wizard to use your own version of GROMACS too, but even that step is optional.
You can:
- Prepare your system (solvation, ion addition, topology generation, etc.)
- Minimize energy
- Equilibrate under NVT and NPT conditions
- Run production MD simulations
- View results as plots and trajectories, fully integrated in SAMSON
Everything is visual and accessible from a series of clear steps inside the interface.
Why it matters
Whether you’re a student learning molecular simulations, a researcher needing quick results, or someone working remotely with limited hardware, having seamless access to GROMACS in the Cloud via SAMSON simplifies your workflow and opens up new possibilities. You can focus on the science — not the setup.
To start using the GROMACS Wizard and learn more about launching systems in the Cloud, visit the full documentation page: GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON at https://www.samson-connect.net.