Setting up molecular dynamics (MD) simulations can be complex and time-consuming, especially when dealing with hardware limitations or compatibility issues. Running simulations on your own machine is not always feasible when dealing with large systems or long simulation times.
If you’re working with GROMACS and want a smoother workflow with the option to offload computation to the cloud, the GROMACS Wizard Extension for SAMSON might be worth exploring.
Through SAMSON, an integrative platform for molecular design, you can easily prepare systems and launch GROMACS simulations not only locally but also in the Cloud — drastically reducing required setup time and computational burden.
Why use the Cloud?
Here are a few reasons why cloud simulation might make sense for your workflow:
- You’re working with large molecular systems that are too slow to simulate on your laptop or workstation.
- You don’t have the time or expertise to install and configure GROMACS on multiple machines.
- You need to run multiple simulations in parallel, which isn’t practical locally.
Simplified Workflow
With the GROMACS Wizard Extension, simulations can be launched directly in the cloud after system preparation — all from within SAMSON. While some simulations may require pre-processing or parameter tuning, many cloud-based runs can be initiated with minimal manual intervention, especially for typical tasks like energy minimization or equilibration.
The extension handles:
- System preparation (solvation, adding ions, etc.)
- Energy minimization
- Equilibration (both NVT and NPT)
- Production MD simulations
- And launching everything in the Cloud
Once computations are running, users can continue working or log back in later to access the completed results: trajectory files, plots, and logs are retrieved automatically.
Zero Manual Installation of GROMACS
The GROMACS Wizard ships with the GROMACS engine (version 2021.3 at the time of writing), so there’s no need to compile or install anything separately. This lowers the entry barrier, especially for users new to MD or those on platforms where scientific software can be hard to configure (e.g., certain Linux installations or macOS).
Use Your Own GROMACS if You Prefer
Some users may still want to use a locally compiled and optimized version of GROMACS (e.g., compiled with GPU support or specific compiler flags). The GROMACS Wizard allows switching between its bundled version and a local installation, giving flexibility for performance tuning while still benefiting from the simplification of the workflow.
Cross-platform Convenience
The extension is available for Windows, Linux, and macOS within SAMSON. Cloud launching capabilities allow users on machines with modest hardware to still access significant computational power.
The GROMACS Wizard offers a streamlined way to integrate cloud computing into your MD simulation workflow — whether you’re running a few trajectories or scaling up your projects.
To learn more about the GROMACS Wizard and launching simulations in the cloud, see 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 download the platform at https://www.samson-connect.net.