For molecular modelers, one recurring challenge is ensuring enough computational power to run molecular dynamics simulations efficiently. This becomes especially pressing when working with large systems or when comparison between multiple parameter combinations is needed. Local machines often fall short, and setting up a high-performance cluster for GROMACS can be technically demanding and time-consuming.
If you’ve ever hesitated to run production-level molecular dynamics simulations because your workstation heats up like a coffee machine—or simply because compiling GROMACS is a task you’d rather avoid—you might want to take a closer look at the Cloud simulation capabilities offered by the GROMACS Wizard Extension in SAMSON.
Simulations in the Cloud: Directly from Your Desktop
The GROMACS Wizard integrates GROMACS capabilities directly into SAMSON, allowing you to set up, run, and analyze simulations with a graphical interface. But one particularly useful (and often overlooked) feature is that you can offload your simulation to the Cloud without needing to configure a remote machine yourself.
This means no manual server setup, no remote compilation, and no SSH key configuration. You just prepare your molecular system using the integrated steps in the GROMACS Wizard and choose to run the simulation in the Cloud instead of locally. Everything else happens behind the scenes.
Why This Matters
- Accessibility: You don’t need to have a powerful local machine. Any computer that can run SAMSON can act as a launchpad.
- No compilation needed: The extension already includes GROMACS (version 2021.3), saving you the often painful process of compiling from source.
- Quick testing: Offload multiple simulations at once and explore different parameters or system states easily. Great for preparing publications or validating hypotheses.
Additionally, the Cloud option isn’t locked into one specific workflow. You still keep the flexibility to define custom index groups or apply tailored simulation parameters before submission. Once the simulation is complete, results—trajectories and plots—are available for analysis within SAMSON’s visualization environment.
Getting Started
The Cloud simulation functionality is just one of many features bundled into the GROMACS Wizard Extension. If you already have SAMSON installed, you can add the extension in one click through SAMSON Connect. You’ll find the launcher for Cloud simulations integrated into the step-by-step workflow: from system preparation to energy minimization, NVT/NPT equilibration, and production runs.
The Cloud option becomes particularly valuable toward the end of the workflow—during the Production Molecular Dynamics Simulation step—where computational demands usually peak. Simply toggle the Cloud option instead of the local one before launching your run, and you’re set.
This feature is available across Windows, MacOS, and Linux, making it broadly accessible across research groups and institutions with varying hardware platforms.
To learn more and explore a detailed tutorial, including other features like umbrella sampling, PMF analysis, and coarse-grained systems, 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 download SAMSON here: https://www.samson-connect.net