HPC on AWS
GROMACS Molecular Dynamics GPU-Optimised HPC Server by Yobitel
The GROMACS GPU-Optimised HPC Server is a ready-to-use solution designed for scientists, researchers, and bioinformatics professionals who run molecular dynamics simulations — fully prepared on AWS with all the tooling needed to run high-performance GPU-accelerated workloads without complex setup.
The GROMACS Molecular Dynamics GPU-Optimised HPC Server is a ready-to-use solution designed for scientists, researchers, and bioinformatics professionals who run molecular dynamics simulations. It comes fully prepared on AWS with all the tools you need to run high-performance GPU-accelerated workloads without any complex setup.
GROMACS is a free and open-source molecular dynamics engine widely used in chemistry, biology, and materials science. Normally, configuring GPU acceleration, MPI, libraries, and remote access can be time-consuming and difficult.
Key Features
- GPU-Accelerated GROMACS Environment: GROMACS compiled with CUDA, OpenMPI and optimised numerical libraries for maximum simulation throughput.
- VMD for Advanced Molecular Visualisation: Pre-installed VMD enables real-time visualisation of trajectories, molecular structures, and simulation outputs directly in the cloud.
- BioBB Modules for Workflow Automation: Includes BioBB libraries to streamline molecular modeling, preparation, analysis, and post-processing workflows through automated scripts.
- Amazon DCV Remote Access: A secure, responsive remote desktop provides direct access to GROMACS, VMD, XMGrace, and the full HPC environment with minimal latency.
- Automated Workflow Setup: Startup scripts automatically initialise GPU settings, environment variables, BioBB modules, and visualisation tools—reducing manual setup and enabling faster simulation launches.
- Lightweight Scientific Desktop: Includes XFCE and terminal automation for a clean, fast, GPU-ready desktop optimised for scientific visualisation and computation.
- Complete Documentation: Step-by-step guidance for launching the instance, accessing DCV, running GPU-enabled GROMACS simulations, using VMD for visualisation, and executing BioBB workflows.
Technical Usage Manual
- Once you subscribe to the AMI for Gromacs from the AWS Marketplace, choose the launch through EC2 and launch.
- It redirects to the launch instance page, configures the required details, i.e., Name, Instance type, Keypair, Network Setting, Storage, and launches the Instance.
- Choose the Instance type as per your requirements.
- When the instance is successfully created, go to the EC2 Dashboard in the AWS Console, select your created instance, and copy the public IP of the instance.
- You can view the generated password under the file “DCV-LOGIN.txt” for your DCV session.
- Use the obtained public IP address from the created instance (Ex, 38.84.57.81)
- Open a web browser. Navigate to: (https://:8443). Replace your instance's public IP in ().
- The Login Page appears for DCV.
- You can view the generated password under the file “DCV-LOGIN.txt” for your DCV session. Username: ubuntu Password: Please check the file “DCV-LOGIN.txt
- Now the Gromacs terminal inside DCV will open.
- Starting in the terminal will launch the GROMACS automation. To modify the input files, use change-inputs instead of Start
- User Can Select which step they need to start.
- Users can manually run both Non-MPI and MPI GROMACS commands by creating the necessary directories, and can also develop automation scripts using BioBB modules, as well as visualise results with VMD and xMGrace
- Users can refer to the official GROMACS tutorials available at MDTutorials (http://www.mdtutorials.com/gmx/) and the GROMACS Tutorials Portal (https://tutorials.gromacs.org/) for step-by-step guidance on molecular dynamics workflows, simulation setup, and analysis procedures.
Insights & Support
- For further details about Gromacs and its uses, refer to the https://www.gromacs.org/ website.
- We will do our best to respond to your questions within the next 24 hours in business days. For any technical support or queries, please contact our Support.
- Please check out our other Containerised Cloud-Native application stacks, such as Blender, Paraview, and Openfoam AMI - Amazon Machine Images- in the AWS Marketplace.
Deploy GROMACS Molecular Dynamics GPU-Optimised HPC Server
One-click deploy from AWS Marketplace into your own AWS account. Your data never leaves your VPC. Billed through your existing AWS account — no separate Yobitel subscription, no procurement overhead.