If you’ve spent hours in a computing cluster queue or had to deal with installation issues for large molecular dynamics packages, you’re not alone. For many molecular modelers, especially those working in academic environments or on personal machines, accessing suitable computational resources can be a persistent challenge.
This is where the GROMACS Wizard Extension in SAMSON becomes particularly helpful. Beyond simply making system prep and simulation seamless, one of the lesser-known but highly practical features of the wizard is the ability to launch GROMACS simulations in the cloud, directly from within SAMSON.
Why run simulations in the cloud?
While GROMACS is highly optimized for speed on local machines, not every research environment comes with access to high-performance setups. Whether your local machine is too weak or you’re running multiple jobs that would clog up your computer, sending tasks to the cloud offers:
- Speed: High-performance nodes can accelerate your work.
- No local setup: You don’t need to preconfigure multiple dependencies or Linux-based clusters.
- Parallel productivity: While one job is running remotely, you can use your machine for other projects.
How it works in SAMSON
Once you’ve installed the GROMACS Wizard Extension in SAMSON, launching a cloud simulation is as straightforward as a few clicks. Here’s a quick overview:
- Prepare your simulation system using the wizard (including energy minimization and equilibration, if needed).
- Go to the
Production MDstep or the relevant computation step in your workflow. - Select the option to Run in the Cloud.
What happens in the background?
When you choose to use the cloud, SAMSON packs your system, sends it securely to the cloud service, and runs your simulation using a GROMACS setup that’s already optimized for that environment. Once the job completes, you’ll automatically receive:
- The simulation trajectory (.xtc files)
- Relevant log and energy files
- Visual plots generated directly from the trajectory
You don’t need to install or compile GROMACS yourself. And better yet, the extension ships with GROMACS 2021.3, while still giving you the option to use your own GROMACS build if desired.
Who benefits most from this?
If you’re working remotely, running educational labs, or managing repetitive simulation tasks, the cloud feature can greatly improve your productivity. It’s also useful if you’re teaching molecular dynamics and want students to run jobs without needing to configure their local environments.
Try it out
To install the extension, just sign in to SAMSON Connect and head over to the Extensions section, where you’ll find the GROMACS Wizard Extension available for Windows, macOS, and Linux.
You can find more detailed steps and options under the Launching computations in the Cloud section of the tutorial.
Learn more: https://documentation.samson-connect.net/tutorials/gromacs-wizard/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.