{"id":12816,"date":"2023-06-01T08:00:00","date_gmt":"2023-06-01T15:00:00","guid":{"rendered":""},"modified":"2024-08-28T12:49:12","modified_gmt":"2024-08-28T19:49:12","slug":"unlocking-the-power-of-azure-for-molecular-dynamics","status":"publish","type":"post","link":"https:\/\/azure.microsoft.com\/en-us\/blog\/quantum\/2023\/06\/01\/unlocking-the-power-of-azure-for-molecular-dynamics\/","title":{"rendered":"Unlocking the power of Azure for Molecular Dynamics"},"content":{"rendered":"\n

More than ever, scientists need new technologies to help solve many of the most pressing issues facing society like reversing climate change, addressing food insecurity, and developing lifesaving therapeutics. Fundamentally, these problems are chemistry and materials science challenges, and some will require the transformational power of a scaled quantum computer. However, given the advancements of classical computing services in the cloud, scientists can start to make rapid progress towards solving these problems today.<\/p>\n\n\n\n

Molecular dynamics (MD)\u2014the simulation of molecular interactions\u2014is one computational problem that pushes the boundaries of what is possible with today\u2019s high-performance computing platforms. More powerful platforms for molecular dynamics simulations could unlock the development of new materials, new drugs, and more efficient batteries, so a team of Azure Quantum<\/a> scientists recently set out to ask a fundamental question: what are Azure\u2019s capabilities for these types of simulations? Here\u2019s what we learned and how any scientist can use Azure to drive similar results today.<\/p>\n\n\n

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Visual representation of Molecular Dynamics simulation (in this example, Satellite Tobacco Mosaic Virus– PBID 7M3T). <\/em> 
Images generated using MOL* 3D viewer on RCSB PDB—<\/em> 3D View (<\/em>source<\/em><\/a>)<\/em> <\/figcaption><\/figure>\n\n\n\n

Azure provides the latest in high-performance computing<\/h2>\n\n\n\n

Molecular dynamics calculations pose unique high-speed communication challenges which require state-of-the-art computing capabilities. The Microsoft Azure cloud architecture helps researchers overcome these hurdles by allowing them to take advantage of the latest software and hardware developments required for chemistry and materials science research. By simplifying the provisioning of the necessary high-performance computing (HPC) resources, Azure helps scientists rapidly deploy and execute complex simulations of the structure and dynamics of macromolecules. This significantly accelerates chemical and materials innovation, for example enabling the creation of better pharmaceuticals by modeling biomolecules and their relevant properties at a faster pace.<\/p>\n\n\n\n

Azure high-performance computing engineers have made significant progress in advancing the scale and networking speeds of the cloud platform. The latest Azure virtual machines use InfiniBand for low-latency communication across distributed nodes for differentiated scalability and performance gains. Our team has demonstrated excellent parallel efficiency and an increase of over 200 percent in benchmark simulations compared to previous virtual machines, particularly for larger simulations.<\/p>\n\n\n\n

Customers are already taking advantage of Azure cloud HPC capabilities today. You can read more <\/em>here.<\/em><\/a><\/p>\n\n\n\n

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\u201cWith Azure HPC, we\u2019ve seen about a 50 percent speedup on some of our chemistry calculations that we run\u2014which is critical for R&D because every second counts, not just for getting the results quickly, but also in terms of cost and throughput.\u201d\u2014<\/em> Glenn Jones, Research Manager at Johnson Matthey Technology Center.<\/em><\/p>\n<\/blockquote>\n\n\n\n

Simulating complex molecular dynamics in Azure enables R&D acceleration<\/h2>\n\n\n\n

Molecular dynamics simulations translate atomic-scale forces and energies into molecular motion and are an important tool for both life sciences and materials science research. In life sciences, for example, molecular dynamics simulations are used to understand proteins, ligands, and their associated properties, which can be used to accelerate the discovery of better pharmaceuticals by modeling drug molecules and their relevant protein binding sites.<\/p>\n\n\n\n

Molecular dynamics workloads stand to greatly benefit from specialized HPC systems whose architectures use both graphics processing units (GPUs) and central processing units (CPUs) with high-speed interconnects between them. Optimized MD simulations pose unique computational challenges related to time scale, sampling, and analysis, requiring powerful computing nodes with low-latency communications\u2014a task for which Azure is uniquely suited.<\/p>\n\n\n\n

Time scale and sampling<\/h3>\n\n\n\n

Biologically relevant events occur across a wide range of timeframes from fractions of a second to decades. Consider an example event that occurs within 1\/1,000th<\/sup> of a second. While this may seem short in real time, it represents a massive computational workload. To capture relevant chemical properties in these simulations, the system needs to compute the position and momentum of all the atoms very frequently. Often, these properties are calculated every 10-12<\/sup> seconds for all atoms in the system. This means one would have to carry out at least a billion calculation steps to perform simulations on the same timescales as the event of interest.<\/p>\n\n\n\n

Powerful computing resources in Azure make this computational problem more tractable. In addition to requiring state-of-the-art processors\u2014including both CPUs and GPUs\u2014to accurately evaluate energies and forces, scalable molecular dynamics simulations need high-performance communication networks, because each calculation step requires messages to be passed between processors to communicate force and energy information. As the number of processors used in the simulation increases, so too does the need for faster communication, since simulation performance is extremely sensitive to the speed at which information can be passed between distributed nodes.<\/p>\n\n\n\n

Analysis<\/h3>\n\n\n\n

The analysis of molecular dynamics simulation trajectories also requires high-performance computing methods. To understand the simulation results, scientists must apply compute-intensive methods to analyze large volumes of trajectory data. This analysis requires advanced statistical methods, high-performance computing platforms, and chemists\u2019 expert knowledge to interpret results.<\/p>\n\n\n\n

InfiniBand acceleration is critical to molecular dynamics simulations<\/h2>\n\n\n\n

Microsoft is committed to making the most advanced computing resources available through Azure cloud services. The Azure cloud HPC platform allows researchers to take advantage of InfiniBand on HB Series virtual machines, which enables low-latency communication across distributed nodes for differentiated scalability and performance boosts.<\/p>\n\n\n\n

We\u2019ve seen strong results using Azure for molecular dynamics:<\/p>\n\n\n\n