One of the most common bottlenecks for molecular modelers is access to sufficient compute power. Many users reach the limits of their local machines when simulating large systems or running long molecular dynamics trajectories. Getting access to high-performance computing often requires technical setup, IT negotiation, and configuration work that distracts from actual scientific research.
If this sounds familiar, the GROMACS Wizard Extension for SAMSON offers a practical, streamlined solution: the ability to run molecular dynamics simulations using GROMACS directly in the Cloud, without leaving the SAMSON interface.
Why run in the Cloud?
Running simulations in the Cloud can:
- Save time by avoiding complicated local setup or configuration
- Enable large or long simulations without local hardware constraints
- Allow you to continue using your workstation for other tasks while simulations run remotely
How it works
The GROMACS Wizard Extension integrates Cloud capabilities so that, after setting up your simulation (preparation, minimization, equilibration), you can choose to dispatch the job to the Cloud rather than running it locally. SAMSON takes care of job submission and retrieval of results so that you can focus on your system and your science.
What do you get back?
Once your simulation completes in the Cloud, you automatically retrieve:
- Simulation trajectories (.xtc, .trr)
- Energy and temperature plots
- Log files and terminal output
All of these are integrated into the SAMSON environment for visualization or further analysis with other extensions.
How to start
To use the Cloud feature:
- Install the GROMACS Wizard Extension
- Prepare your molecular system within SAMSON using the wizard steps
- In the final step, choose to launch your simulation in the Cloud instead of locally
Once submitted, you can monitor progress and receive notifications when your simulation is complete.
Who is it for?
This feature is especially useful for students, academic researchers, and educational institutions that want to perform GROMACS molecular dynamics simulations without investing in expensive infrastructure or writing deployment scripts.
Where to learn more
You can dive into the documentation and find step-by-step instructions on launching computations in the Cloud here: Launching computations in the Cloud.
Or see the complete GROMACS Wizard documentation page at:
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