NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach 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 500,000 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.

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Other Spotlights 

Spotlight: Spray Against Flu (Jan 2014)

Lung surfactant protein, an influenza virus inhibitor

image size: 199.7KB
made with VMD

Our body uses several defense mechanisms against seasonal flu, the common affliction caused by influenza viruses. By taking a yearly flu shot, our body's defense based on antibodies is trained and envoked. A defense system not based on antibodies acts at the very front line of influenza virus attack, namely the lungs. For this protection the body uses so-called lung surfactant proteins that coat the inner lining of the lungs to keep a wet film on the lung surface needed for oxygen-carbon dioxide exchange. The lung surfactant proteins also serve as police against influenza viruses. For this purpose the lung surfactant protein D (SP-D) recognizes a protein component of the virus surface, namely hemagglutinin, and handcuffs the sugar molecules bound to hemagglutinin. A previous experimental-simulation study (see October 2012 highlight) found that SP-D of pigs exhibits a stronger inhibitory activity against influenza A virus in this regard than does human SP-D. In a recent study, researchers have now boosted the protective ability of human SP-D by introducing mutations. Molecular dynamics simulations using NAMD suggest that the mutated human SP-D employs a different and stronger blocking mechanism on the active site of influenza A virus than native SP-D does. Combined with experimental results, the simulations suggest a mechanism through which SP-D acts, namely, by handcuffing viruses together and, thereby, preventing viral entry into cells. The findings from this research might lead to a new protection against seasonal flu, namely a nasal spray containing mutated lung surfactant proteins that strengthen a person's armada of defense proteins on the lung surface. More on our lung surfactant protein website.

Overview

Why NAMD? (in pictures)
How to Cite NAMD
Features and Capabilities
Performance Benchmarks
Publications and Citations
Credits and Development Team

Availability

Read the License
Download NAMD Binaries (also VMD)
Build from Source Code - Git access now available
Run at NCSA, SDSC, NICS, or Texas

Training

Enhanced Sampling and Free-Energy Workshop (Sept 25-29, 2017)
    Held in Urbana, IL. Apply by August 11.
"Hands-On" Workshop in Pittsburgh (May 30-June 2, 2017)
NAMD Developer Workshop in Chicago (May 22-23, 2017)
Charm++ Workshop in Urbana (April 17-19, 2017)
"Hands-On" Workshop in Urbana (April 17-21, 2017)
PRACE School on HPC for Life Sciences (April 10-13, 2017)
Older "Hands-On" Workshops

Support

Having Problems with NAMD?

NAMD Wiki (Recent Changes)
  
NAMD-L Mailing List (Archive)
  
Tutorial-L Mailing List (Archive)
  

Mailing List Issues for Yahoo.com Addresses

Announcements

NAMD 2.13 New Features
One-click NAMD/VMD in the cloud
QM/MM Interface to MOPAC and ORCA
QwikMD GUI Released in VMD 1.9.3
NAMD 2.12 New Features
NAMD 2.12 Release (Dec 2016)
2016 User Survey Report
Previous Announcements

Documentation

NAMD 2.12 User's Guide
   
  (also 773k HTML or 1.1M PDF)
NAMD 2.12 Release Notes
Running Charm++ Programs (including NAMD)
Running GPU-Accelerated NAMD (from NVIDIA)
Introductory NAMD Tutorials
All NAMD & VMD Tutorials
  

Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation

News

Opening New Frontiers in the Battle Against HIV/AIDS
HIV Capsid Interacting with Environment
Assembling Life's Molecular Motor
Membrane Channel Made of DNA Origami
NAMD Paper Has 6000 Citations
Antibiotic Resistance Through Efflux Pumps
Membrane Protein Breakthrough
Massive Flu Virus Simulations
Ion Channels in General Anesthesia
How HIV Defeats Cellular Defender
Older News Items