NAMD

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Parallel Programming Laboratory

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 cores for typical simulations and beyond 200,000 cores for the largest simulations. 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.

Want to make NAMD and VMD better? Join our team! We are hiring a research programmer. Apply by May 20.

The 2005 reference paper Scalable molecular dynamics with NAMD has over 1000 citations as of March 2010.

Other Spotlights

Spotlight: Shield Against Influenza (Oct 2012)

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made with VMD

The fall flu season is coming. It is time to get your flu shot! Many people may still remember the influenza A H1N1 flu ("swine flu") pandemic of 2009, which caused 280,000 deaths worldwide. The best way to prevent the flu is to get vaccinated with a flu shot or use the flu nasal spray vaccine. However, rapid evolution of the flu virus constantly requires new vaccines. Fortunately, the immune system has several defensive mechanisms in the lung to clear inhaled pathogens. One of these mechanisms involves surfactant proteins which induce aggregation of viral particles and, thereby, prevent infection, serving as a front-line host defense. Recently, researchers found that surfactant protein D (SP-D) from pigs exhibits particularly strong inhibitory activity, more so that human SP-D. This discovery leads researchers to investigate SP-D structure-related antiviral activity. In a recent experimental-simulation study, crystallographic analysis of pig and human SP-D showed that a loop involved in viral binding on pig SP-D is longer than the respective loop on human SP-D; molecular dynamics simulation revealed that the longer loop of pig SP-D has higher flexibility than that of human SP-D, suggesting that the flexible loop region could facilitate strong binding of SP-D to virus. Based on this finding, one can develop new nasal spray anti-flu protection through other structural modification of human lung surfactant proteins. More on our lung surfactant protein website.

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Announcements

NAMD 2.9 New Features
NAMD 2.9 (April 2012)
2011 User Survey Report
NAMD 2.8 New Features
NAMD 2.8 (May 2011)
NAMD 2.7 New Features
NAMD 2.7 (Oct 2010)
How to Cite NAMD
Previous Announcements

Documentation

Adaptive Biasing Force Website
Interactive Molecular Dynamics Tutorial
Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation

News

Poliovirus Simulated on BlueGene/Q
Virus Structure Determined with Blue Waters
Kale, Schulten Win Fernback Award
Making History on Blue Waters
Hello Siri, Please Start My Experiment Now
Blue Waters Early Science System
Proteins Help DNA Replicate Past Damage
SC11: Scaling to 100 Million Atoms
Copper Folds Parkinson's Plaques
Mechanics of Membrane Proteins
Molecular Mystery of Blood Clotting
Alzheimer's Misfolding Simulated
When Cellular Bones Soften
Getting the Rabbit in the Hat
Insights Into Deafness
Molecular Machines Replicate and Repair DNA
Sound Science
Blueprint for the Affordable Genome
Mechanics of Hearing and Deafness
NAMD Paper Has 1000 Citations
Closing the Gaps
Inside the Swine Flu Virus
GPU Acceleration in Development
NCSA IACAT to Accelerate NAMD
Parkinson's, Alzheimer's Diseases
Knock, Knock, Who's There?
Step Up to the BAR Domain
Older News Items

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