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: Molecular Mechanism of Influenza Drug Resistance (Oct 2010)

Tamiflu Binding Pathway

image size: 483.2KB
made with VMD
movie: Windows AVI or Apple MOV

Fever, chills, sore throat, coughing, aches, and pains? Ah ..... you have the flu! As a measure of prevention, vaccines against seasonal influenza are distributed and administered each fall. Last year though, the outbreak of the H1N1pdm "swine" influenza virus, caught health workers by surprise as this virus not only infected individuals during the spring and summer months, but also seemed to be particularly virulent towards otherwise healthy young people. Even more alarming was increasing evidence that H1N1pdm had acquired resistance to the frontline antiflu drug, Tamiflu. In response to this, computational biologists at the University of Illinois and the University of Utah teamed up to uncover the basis for influenza drug resistance through quantum chemistry, and molecular dynamics simulations with NAMD. The results of this study have recently been reported, and uncovered a two stage binding pathway for Tamiflu in H1N1pdm "swine" and H5N1 "avian" flu proteins, as well as a possible mechanism through which genetic mutations can induce drug resistance in one of the stages. Subsequent efforts at drug design against influenza can take advantage of this discovery. This discovery was made possible through use of so-called GPU computing (see Oct 2007 highlight "Graphics Processors Speed Up Simulations"). More information can be found here.

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 10-14, 2018)
NAMD Developer Workshop in Urbana (June 11-12, 2018)
"Hands-On" Workshop in Pittsburgh (May 21-25, 2018)
Charm++ Workshop in Urbana (April 11-12, 2018)
"Hands-On" QM/MM Simulation Workshop (April 5-7, 2018)
Enhanced Sampling and Free-Energy Workshop (Sept 25-29, 2017)
"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

Supercomputing HIV-1 Replication
Computational Microscope Gets Subatomic Resolution
Early Science Project on First US Exascale Machine
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