GROMACS Molecular Dynamics GPU-Optimised HPC Server by Yobitel

syedaqthardeen
3 days ago
2 min read

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://<EC2_PUBLIC_IP>:8443). Replace your instance's public IP in (<EC2_PUBLIC_IP>).
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.