Setting up and running molecular dynamics (MD) simulations with GROMACS can be demanding in terms of both time and computational resources. If you’re working with large systems, using a laptop or a local workstation might not be efficient enough. Fortunately, the GROMACS Wizard Extension for SAMSON makes it possible to offload GROMACS computations to the Cloud, helping researchers and modelers streamline their workflow without worrying about installing HPC environments.
In this post, we’ll look at the built-in support for cloud-based GROMACS simulations in the GROMACS Wizard Extension: what it offers, why it matters, and how it can save time and effort.
Why launch simulations in the Cloud?
Cloud-based MD simulations offer several advantages:
- No local performance bottlenecks: Run long simulations without overloading your machine.
- Parallel processing: Use virtual machines with more cores to accelerate simulations.
- No installation overhead: No need to build custom MPI-enabled GROMACS installations locally.
Despite these benefits, many users hesitate to move computations to the Cloud due to the complexity of setup. The GROMACS Wizard Extension addresses this by providing a simple, integrated interface for launching Cloud jobs.
How it works in SAMSON
Once the GROMACS Wizard Extension is installed in SAMSON, you can prepare your system through the step-by-step wizard interface (e.g., energy minimization, NVT/NPT equilibration). When it comes time to launch the production MD simulation, you can choose where the simulation runs: locally or in the Cloud.
The Cloud-launch capability is fully integrated into the simulation workflow. With just a few additional input parameters (e.g., duration of simulation, number of nodes), the Extension will:
- Package the necessary input files
- Send them to the appropriate Cloud environment
- Run the GROMACS job remotely
- Retrieve trajectories and analysis results once complete
An example use case: You’ve set up a protein-ligand complex and want to run a 100 ns simulation. Rather than waiting hours or days for it to run on your laptop, you could launch it in the Cloud before leaving the lab—and return the next morning to analyze the results.
Who this is for
This feature is especially valuable for:
- Students and researchers without access to high-performance computing clusters
- Teams working remotely who need a consistent, reproducible platform
- Early-stage modelers experimenting with simulation parameters
And because GROMACS ships with the extension, installation concerns are minimal—you don’t need to compile the software yourself, nor worry about missing dependencies or GPUs.
Getting started
Launching computations in the Cloud is just one of the many features of the GROMACS Wizard Extension. It’s available on Windows, Linux, and MacOS, and integrates fully with SAMSON’s modular interface. If you’d prefer, you’re also free to run simulations locally or use a custom GROMACS build tuned to your system.
To try it out, make sure you have the Extension installed and follow the Cloud job instructions in the full tutorial here: 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.