Running molecular dynamics (MD) simulations using GROMACS can be computationally demanding. Whether you’re studying protein folding, drug binding, or materials at the atomic level, the need for high-performance resources often causes significant delays or bottlenecks. This is especially true when working with large systems or during the production phases of simulations.
The good news: the GROMACS Wizard Extension for SAMSON offers a straightforward way to run MD simulations in the Cloud—helping you overcome hardware limitations and finish computations faster.
Why consider using the Cloud?
If you’re using your personal workstation for MD, chances are you’ve had to wait hours (or even days) for a simulation to finish. Or maybe you’ve dealt with complicated GROMACS installations and setup on HPC clusters. Using the Cloud shifts the computational load away from your machine, and lets you:
- Run intensive simulations without slowing down your local work.
- Test longer production runs or high-resolution simulations.
- Work from any platform (Windows, Linux, MacOS) while leveraging external compute power.
How does SAMSON simplify Cloud simulation with GROMACS?
With the GROMACS Wizard in SAMSON, the entire process—from system preparation to launching a simulation in the Cloud—has been streamlined. There is no command-line setup or server configuration. The Wizard guides you through each MD step (energy minimization, equilibration, production runs) and includes an option to easily offload computation to the Cloud.
Here’s how it works:
- Use the GROMACS Wizard to build and prepare your molecular system directly inside SAMSON’s graphical interface.
- Choose to run locally or launch in the Cloud from within the same interface.
- Your simulation is handled securely, and results (trajectories, log files, plots) are automatically downloaded to your session for visualization and analysis.
Do I need to install GROMACS?
No. The extension includes the latest GROMACS version (2021.3 at the time of writing), so you don’t need to install or compile anything separately. This also avoids version mismatches or build errors that can arise when setting up GROMACS on your own.
Prefer to use your own GROMACS build?
You still can! The extension gives you the option to link a custom local GROMACS installation. This is especially useful if you’ve optimized your build for specific CPU instructions or GPU acceleration.
Getting started
To explore Cloud simulations with GROMACS Wizard:
- Install the GROMACS Wizard Extension via the SAMSON Connect platform.
- Prepare your system and choose the Cloud option when launching your simulation.
Whether you’re a student or researcher, this workflow is especially helpful when your simulation needs go beyond what your laptop or desktop can handle.
To learn more about Cloud-based MD simulations and the full workflow using the GROMACS Wizard in SAMSON, visit the official documentation page here: 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.