One frequent bottleneck in molecular modeling is computational power. While modern desktops can handle many local simulations, certain tasks such as large-scale MD simulations, enhanced sampling, or batch computations demand more resources. This is where cloud computing becomes a valuable tool.
The GROMACS Wizard Extension in SAMSON provides built-in support to run GROMACS simulations not only locally, but also in the Cloud. This makes it easier for users — especially those without high-end hardware — to perform complex molecular dynamics without complex cloud setups or manual configuration.
This blog post walks you through how SAMSON integrates GROMACS cloud simulations and how it can help you work more efficiently.
Why use the cloud for MD simulations?
Cloud resources offer flexibility, scalability, and speed. If you’re dealing with:
- Long production runs that would block your workstation for days
- Umbrella sampling across multiple reaction coordinates
- Batch computations for screening or ensemble simulations
- A need for parallel simulations to explore multiple conditions or replicas
…then offloading simulations to the Cloud can be a practical solution.
Cloud simulation from SAMSON: No server setup required
With the GROMACS Wizard Extension, SAMSON simplifies cloud-based computation. Everything happens through the graphical interface — no need to manually configure clusters or install dependencies. The extension ships with GROMACS 2021.3 embedded, and you can choose whether to use this built-in version or your own local GROMACS build.
Launching a cloud job is as simple as preparing the simulation locally, then selecting the Cloud option when running the simulation. The results — including trajectory files and plots — are then returned to your SAMSON session for visualization and analysis.
Users retain full control over simulation parameters. This includes pre-processing steps, forcefield selection, and MD protocol customization (e.g., NVT/NPT, production, or umbrella sampling).
Example workflow: local preparation + cloud run
For example, you might prepare a protein-ligand system in SAMSON using the GROMACS Wizard:
- Build or import your molecular system in SAMSON
- Use the Wizard to set up and visualize your system (charges, solvation, minimization)
- For simulation, choose the Cloud execution mode
- Wait for the results — snapshots and trajectories will be returned and automatically opened in SAMSON
This solves a key problem: Instead of waiting hours or days on an overloaded workstation, you complete the process in less time while still retaining interactive control and visual output.
Use cases and availability
Whether you’re a student working from a laptop, a beginner interested in learning MD simulation without setup frustrations, or a modeler needing to offload time-consuming calculations, cloud-based simulation in SAMSON helps balance simplicity and power.
The GROMACS Wizard Extension is compatible with Windows, macOS, and Linux, and integrates seamlessly with other SAMSON tools.
To learn more, visit the full documentation page for the GROMACS Wizard Extension: 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.