Many molecular modelers work with simulation setups that are too large or too computationally expensive to be run comfortably on their local machines. While GROMACS is efficient, setting up a local high-performance computing environment—and maintaining it—is not ideal for many researchers or students. Fortunately, SAMSON’s GROMACS Wizard Extension offers a straightforward way to run GROMACS simulations in the cloud, without advanced IT knowledge or complicated cloud setups.
Here we’ll explore how the GROMACS Wizard lets you prepare and launch molecular dynamics (MD) simulations on the cloud directly from within SAMSON’s graphical interface. This is particularly helpful when your local system is busy, limited in computational power, or you need to run several simulations in parallel.
Why the Cloud?
Cloud computing provides access to powerful machines with more memory, compute cores, and GPU acceleration. However, working with cloud-based GROMACS simulations typically requires major configuration: installing libraries and tools, setting up SSH keys, managing storage, and handling remote job scripts. This can make it inaccessible to many researchers.
The GROMACS Wizard Extension removes that complexity. Once installed in SAMSON, it allows you to upload and run simulations in the cloud with a few clicks, and then retrieve the results, including trajectory files and performance plots, for further analysis.
How it Works in SAMSON
Launching computations in the cloud can be done from the same interface you’re already using to setup your MD system locally. Here’s an outline of the process:
- Prepare your molecular system in SAMSON using the GROMACS Wizard steps (e.g., solvation, energy minimization).
- Navigate to the cloud configuration section of the Wizard.
- Choose your simulation parameters as you would normally do for a local run.
- Select the option to run in the cloud. SAMSON will handle packaging the data, sending it to the cloud, and starting the simulation.
- Once completed, you can retrieve simulation results with a single click.
This integrated pipeline means you don’t have to worry about compatibility issues, scripting errors, or managing remote resources. It’s especially convenient for batch computations or when you want to use scalable compute resources on demand.
Who Is This Useful For?
Cloud-based simulation can be a good fit if:
- Your local computer cannot handle long or complex simulations.
- You need results quickly and want to run multiple simulations at once.
- You want to avoid managing GROMACS installations or dependencies on a server.
SAMSON even allows you to use your preferred version of GROMACS in the cloud, or stick to the pre-packaged one for ease of use.
To explore cloud simulations and other GROMACS Wizard capabilities, visit the full documentation: 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.