NAMD (Nanoscale Molecular Dynamics)

Overview

Every facet of our physical world is determined by the behaviors, properties, and interactions of the microscopic particles that make up all materials. Perhaps nowhere is this more evident than with the inner workings of biological organisms. Our understanding of all living things originates at the molecular level. Vastly complex arrangements of interconnected chemical systems combine to create the emergent phenomenon that we call life. Sadly, these systems do not always function correctly. They can break down over time, succumb to an invading attacker, or corrupt themselves from within. 

The first step in treating any disease is understanding what is going on, and for the most difficult medical challenges that humanity faces today, one key approach is modeling the molecular systems directly using computer simulations. This poses its own challenges: simulating a process effectively could require tracking millions or billions of atoms, over extended durations, with time intervals of important activity significantly more fleeting and numerous than human perception can comprehend. Moreover, interactions between molecules are not consistently distributed among either space or time. 

All-atom model of the HIV capsid

This video was made with VMD and is owned by the Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign.

The combination of large amounts of fine-grained work units together with imbalance among that work presents a problem to computer simulation architects: How can a real-world computing cluster perform these computations effectively? Fortunately, NAMD is the most longstanding user of the Charm++ runtime system, which allows it to surmount the challenges of such highly dense and dynamic workloads, relieving chemists and biologists of the burden of distributed-systems programming, and bringing these simulations within the realm of feasibility.

Software

NAMD is one of the most popular and best-performing molecular dynamics simulation software, with over 100,000 users worldwide. With development led by Prof. Klaus Schulten at the University of Illinois at Urbana-Champaign in the 1990s, it is one of the most widely used tools for understanding diseases at a molecular level. NAMD can be used on a wide range of devices, from the most portable tablets and laptops, all the way up to the largest supercomputers in the world.

These images were made with VMD and are owned by the Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign.

NAMD is most well-known for its use in modeling the first HIV capsid, which has helped identify new ways to create life-saving therapies for HIV/AIDS patients. As described in Nature in 2013, the HIV capsid contains genetic material for the virus as it enters the cell. When cells are infected, the capsid bursts open, allowing the virus to begin replicating. By understanding the structure and mechanisms of the HIV capsid, scientists can develop ways to prevent the capsid from releasing genetic material, effectively stopping the virus in its tracks. Achieving this lofty goal requires significant computing power to simulate the millions of atoms that make up the HIV capsid, as well as an effective framework to attain efficient parallel performance. The object-oriented, highly scalable parallel programming framework of Charm++ was the perfect fit to achieve these goals. 

NAMD is most well-known for its use in modeling the first HIV capsid, which has helped identify new ways to create life-saving therapies for HIV/AIDS patients. As described in Nature in 2013, the HIV capsid contains genetic material for the virus as it enters the cell. When cells are infected, the capsid bursts open, allowing the virus to begin replicating. By understanding the structure and mechanisms of the HIV capsid, scientists can develop ways to prevent the capsid from releasing genetic material, effectively stopping the virus in its tracks. Achieving this lofty goal requires significant computing power to simulate the

millions of atoms that make up the HIV capsid, as well as an effective framework to attain efficient parallel performance. The object-oriented, highly scalable parallel programming framework of Charm++ was the perfect fit to achieve these goals.

More recently, NAMD has been used for groundbreaking coronavirus simulations as part of a world-wide effort to stymie the spread of COVID-19. The Amaro Lab of UC San Diego is using NAMD to build the first complete model of the SARS-COV-2 coronavirus envelope, to help scientists understand how the virus interacts with receptors within the host cell membrane. The simulation for this model, which is anticipated to contain 200 million atoms, ran on 4,000 cores of the Frontera supercomputer in March of 2020. These simulations can help scientists better understand how to design new drug treatments to more effectively treat those infected with the virus.

Learn more about NAMD

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