One of the common pain points for researchers and students working in molecular modeling is the limited computational power available on their local machines. Whether it’s a laptop with modest specs or a workstation already handling heavy tasks, running molecular dynamics simulations can be time-consuming and resource-intensive. Fortunately, there’s an efficient solution for those using GROMACS within the SAMSON platform: running simulations in the Cloud.
The GROMACS Wizard Extension in SAMSON allows you to launch simulations using the GROMACS engine both locally and in the Cloud. This can significantly reduce waiting time and free your local resources for other tasks. Everything is integrated, so this can be achieved with just a few clicks from within the SAMSON interface.
Why run GROMACS in the Cloud?
When working on large systems or running multiple simulations (e.g., parameter sweeps, umbrella sampling windows, or batch jobs), demand on computational resources can become a bottleneck. Cloud computing provides on-demand access to powerful resources, which is especially valuable for:
- Simulating larger and more complex biomolecular systems
- Running multiple simulations in parallel
- Avoiding long computation times on personal machines
How it works in SAMSON
The GROMACS Wizard Extension in SAMSON abstracts away much of the complexity. You can set up the system, prepare input files, and configure simulation parameters through a graphical interface. Once everything is ready, simply choose the cloud option when launching the simulation. SAMSON handles uploading the required files, running the job remotely using the integrated GROMACS engine, and fetching the results.
Results, such as trajectories and plots, are automatically retrieved and can be explored directly in SAMSON. Because GROMACS is built into the extension (version 2021.3 in the latest release), there’s no need to compile or install it manually either locally or remotely.
This feature is especially useful when combined with SAMSON’s other GROMACS-related capabilities, such as batch computations and PMF analysis. Moreover, you retain the flexibility to still use your local GROMACS installation for comparison or performance tuning.
Platform availability
The GROMACS Wizard Extension is available on Windows, Linux, and macOS, making it cross-platform and accessible to a broad community of users.
For detailed steps on launching simulations in the Cloud, refer to the Cloud computing section of the official documentation.
To explore the full capabilities of the GROMACS Wizard Extension in SAMSON, check the comprehensive tutorial at the official GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.