For many molecular modelers, setting up and running molecular dynamics simulations with GROMACS can be a balancing act between simulation precision and computing power. While local machines often serve well for small systems or short simulations, more complex or longer simulations can easily overwhelm local hardware or queue times on institutional clusters.
The GROMACS Wizard Extension for SAMSON offers a practical solution to this challenge: the ability to launch GROMACS simulations directly in the Cloud, integrated within a visual modeling environment. This simplifies remote computational workflows, allowing you to focus more on your system and science, and less on infrastructure.
Simplifying Remote Simulations
Launching a GROMACS simulation in the Cloud from SAMSON is straightforward. After preparing your system just as you would for a local run (including equilibration and custom settings, if needed), you can configure the simulation to be executed in the Cloud with just a few additional clicks.
This feature integrates neatly into the standard GROMACS Wizard workflow and can handle all stages such as energy minimization, NVT and NPT equilibration, and production MD. Once the simulation is completed, the results — including trajectories and plots — are downloaded back into your SAMSON session for analysis and visualization.
Who This Helps
This Cloud launch feature is especially useful if:
- You are limited by your local machine’s CPU/GPU resources
- You don’t have easy access to a dedicated compute cluster
- You want to offload long or computationally intensive jobs
- You’d like to parallelize simulations — for example, parameter sweeps or batch jobs — without managing remote terminals
No Installation Headaches
The wizard ships with GROMACS (version 2021.3 as of the latest update), meaning you don’t need to worry about installing or compiling anything. However, if you prefer using your own local installation of GROMACS — perhaps one optimized for your hardware — that’s also an option. This flexibility adds to the appeal for both beginners and experienced users.
How to Get Started
To begin, install the GROMACS Wizard Extension via SAMSON Connect. Once installed, you’ll find everything you need under the Biology section in the SAMSON interface. Cloud simulation options become available as part of your normal simulation workflow when using the wizard.
While the Cloud provider details are managed internally by the extension, your simulations benefit from offloading computations, freeing your machine and enabling smooth multitasking. With this model, even resource-intensive tasks such as pulling simulations or umbrella sampling become more accessible to those without dedicated hardware.
Whether you’re exploring coarse-grained models or evaluating potential of mean force, this integrated Cloud feature allows for greater flexibility and scalability.
To learn more about running GROMACS simulations in the Cloud through SAMSON, visit the full documentation page: 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.