Running molecular dynamics (MD) simulations with GROMACS usually requires not just scientific knowledge, but also technical setup: compiling software, configuring command-line commands, managing dependencies, and securing enough computing resources. This can be a challenge — especially when you just want to focus on your molecules and mechanisms.
The GROMACS Wizard Extension in SAMSON offers a practical alternative. It integrates key parts of GROMACS into SAMSON’s user interface, and notably, includes the ability to launch simulations in the Cloud. This is a useful feature if you need to run time-consuming simulations but don’t have local high-performance computing power.
Why Cloud?
Your laptop is a great place to build a system, prepare a structure, or analyze a trajectory — but lengthy production MD simulations? Not so much. With the GROMACS Wizard, you don’t need to transfer files, log into remote environments, or manage GROMACS builds on a remote machine. Instead, the simulation can be started directly in the Cloud from the same interface you use locally.
How It Works
Once you’ve set up your system with the usual MD preparation stages (solvation, minimization, equilibration), you can choose to run the production MD simulation in the Cloud. While the extension ships with GROMACS 2021.3 pre-configured, Cloud jobs can be executed with no additional setup.
This also allows you to multitask: for example, continue working on other projects in SAMSON while a simulation runs externally.
Simplified Workflow
- Prepare and set up your molecular system in SAMSON.
- Select your simulation parameters as you normally would using the GROMACS Wizard Extension.
- Choose the option to run in the Cloud.
- Monitor progress and retrieve your trajectory and plots once the simulation completes.
The interface helps avoid the manual steps typically needed to prepare a simulation for HPC or Cloud environments, such as writing batch scripts or handling remote dependencies.
When Is Cloud Simulation Most Useful?
Here are common scenarios where the Cloud option saves time and frustration:
- You do not have GROMACS installed or tuned on your local hardware.
- You’re on a Mac or Windows laptop with limited compute power.
- You’re screening multiple systems in parallel, and batch processing locally isn’t viable.
- You want faster turnaround or efficient use of offline time.
Getting Started
You can launch a Cloud simulation from the GROMACS Wizard interface in just a few steps. No scripting, no server login — and the data returns neatly into your SAMSON project. If you’ve experienced the frustration of interrupted local simulations or system instability during long runs, offloading to the Cloud can be a practical and time-saving solution.
To learn more about this and other features of the GROMACS Wizard Extension, visit the full tutorial at: https://documentation.samson-connect.net/tutorials/gromacs-wizard/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.