NAMD - Scalable Molecular Dynamics

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Parallel Programming Laboratory

Bionumerics Research Group

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

NAMD reference paper: Scalable molecular dynamics with NAMD.

Other Spotlights

Spotlight: Probing Parkinson's (Apr 2007)

SDSC News Release: SDSC and UC San Diego researchers are using NAMD to zero in on the causes of Parkinson's disease, Alzheimer's disease, rheumatoid arthritis and other diseases. The April 2007 FEBS Journal cover story offers—for the first time—a model for the complex process of aggregation of a protein known as alpha-synuclein, which in turn leads to harmful ring-like or pore-like structures in human membranes, the kind of damage found in Parkinson's and Alzheimer's patients. The researchers also found that the destructive properties of alpha-synuclein can be blocked by beta-synuclein—a finding that could lead to treatments for many debilitating diseases.

Lead author Igor Tsigelny, SDSC researcher and project scientist in chemistry and biochemistry at UCSD, said that the team's research helped confirm what researchers had suspected. “The present study—using molecular modeling and molecular dynamics simulations in combination with biochemical and ultrastructural analysis—shows that alpha-synuclein can lead to the formation of pore-like structures on membranes.” In contrast, he said, “beta-synuclein appears to block the propagation of alpha-synucleins into harmful structures.”

“This is one of the first studies to use supercomputers to model how alpha-synuclein complexes damage the cells, and how that could be blocked,” said Eliezer Masliah, professor of neurosciences and pathology at UC San Diego. “We believe that these ring- or pore-like structures might be deleterious to the cells, and we have a unique opportunity to better understand how alpha-synuclein is involved in the pathogenesis of Parkinson's disease, and how to reverse this process.”

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Spotlight: Probing Parkinson's (Apr 2007)

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