One of the most common challenges for molecular modelers is setting up and running molecular dynamics (MD) simulations efficiently—especially when using powerful tools like GROMACS. While GROMACS is a widely respected package in computational chemistry, getting it installed and optimized on a local machine can be time-consuming, particularly for new users or those working on diverse systems (Windows, Linux, MacOS).
The GROMACS Wizard Extension for SAMSON offers a way to streamline this process, including something many modelers will find immediately attractive: the option to run GROMACS simulations in the Cloud, easily and without compiling or configuring a local GROMACS installation.
Why cloud execution matters
Let’s say you’re preparing a long-timescale simulation, or you’re working on a system with a complex force field that requires significant computational resources. Maybe your own computer slows down too much when running GROMACS locally, or maybe it doesn’t have the optimized version needed for your molecular system.
This is where the GROMACS Wizard comes into play—it gives you the choice to run GROMACS simulations directly in the Cloud, removing concerns about installation, drivers, performance configuration, or even OS compatibility. This can be a valuable time-saver, and it enables researchers to scale simulations without investing in additional hardware or wasting time setting up environments.
How it works inside SAMSON
Once you’ve installed the GROMACS Wizard Extension (available on all major operating systems), launch SAMSON and start preparing your system. The workflow consists of pre-processing, preparation, energy minimization, NVT/NPT equilibration, and production MD simulation. After setup, users can choose whether to run simulations locally—or send them to the Cloud.
To launch a cloud computation:
- Ensure your SAMSON and GROMACS Wizard Extension are up to date.
- Follow the step-by-step system preparation in the wizard interface.
- Choose the Launch in the Cloud option during the execution phase.
- Your simulation is then offloaded to a cloud backend, and results are retrieved inside SAMSON once complete.
This allows you to free up your machine for other tasks, or simply avoid performance trade-offs during computation-heavy runs. Users can also still view trajectories and plots upon completion, directly within SAMSON’s visualization environment.
Do I need to install GROMACS?
No. The extension ships with GROMACS 2021.3, meaning you don’t need to compile GROMACS yourself. However, if you have a custom-built version of GROMACS installed for optimized performance on your system, SAMSON gives you the flexibility to use that as well.
Who is this for?
This cloud-based workflow is particularly helpful for:
- Students learning molecular dynamics simulations who don’t want to deal with installation issues.
- Researchers working across multiple systems (e.g., laptops and desktops with varying OSes).
- Those running long simulations who want to offload the processing.
To learn more about the GROMACS Wizard Extension and how to launch simulations in the Cloud, visit the official GROMACS Wizard Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download and install SAMSON at www.samson-connect.net.