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 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.

The 2005 reference paper Scalable molecular dynamics with NAMD has over 3000 citations as of July 2013.

Wit, grit and a supercomputer yield chemical structure of HIV capsid (article referring to NAMD simulations on Blue Waters reported in Zhao et al., Nature, 497:643-646, 2013.)

Rapid parameterization of small molecules using the force field toolkit, JCC, 2013.

HPCwire Editors' Choice Award: Best use of HPC in life sciences

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Other Spotlights 

Spotlight: Finding the End (July 2013)

RHDV

image size: 651.0KB
made with VMD

DNA, a long linear molecule, is the carrier of genetic information. In the cell, each DNA molecule is packaged in a structure called chromosome. The ends of linear chromosomes are capped by structures known as telomeres to prevent fusion with neighboring chromosomes. Telomeres are maintained by an enzyme called telomerase during DNA replication. In order to do so, telomerase has to find the telomere region on DNA quickly and precisely. One telomerase is the protelomerase TelK, which binds to the ends of DNA, cleaves DNA strands and refolds cleaved DNA ends into hairpin telomeres in linear chromosomes of prokaryotes and viruses. Previous studies have shown that TelK is only active as a dimer. In a recent study, researchers investigated the target-search mechanism of protelomerase TelK through single-molecule experiments and molecular dynamics simulation. It was revealed that as a monomer, TelK undergoes one-dimensional diffusion along non-specific DNA (without telomere sequence), and is able to bind to the target site preferentially. There, the target-immobilized monomer waits for a second binding partner to form an active protein complex. More on our TelK website.

Overview

Having Problems with NAMD?
Why NAMD? (in pictures)
Molecular Dynamics Flexible Fitting
Steered Molecular Dynamics
Interactive Molecular Dynamics
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
Run at NCSA, SDSC, NICS, or Texas

Training


"Hands-On" Workshop in Bremen (June 16-20, 2014)
Charm++ Workshop in Urbana (April 29-30, 2014)
Cryo-EM Modeling Workshop in Urbana (Jan 8-10, 2014)
"Hands-On" Workshop in Urbana (Nov 18-22, 2013)
GPU Programming Workshop in Urbana (Aug 2-4, 2013)
"Hands-On" Workshop in Pittsburgh (June 10-14, 2013)
Charm++ Workshop in Urbana (April 15-16, 2013)
"Hands-On" Workshop in Urbana (Oct 22-26, 2012)
In-Residence Training in Urbana (July 16-27, 2012)
Charm++ Workshop in Urbana (May 7-9, 2012)
Membrane Protein Modeling Workshop in Chicago (May 1-2, 2012)
"Hands-On" Workshop in Urbana (Feb 11-15, 2012)
"Hands-On" Computational Biophysics Workshops
Older 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 2.10 New Features
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

NAMD 2.9 User's Guide
   
  (also 607k HTML or 1019k PDF)
NAMD 2.9 Release Notes
Running Charm++ Programs (including NAMD)
Post-Release Updates on NAMD Wiki
Introductory NAMD Tutorials
Introductory VMD Tutorials
Free Energy Tutorials
Specialized Topic Tutorials
Bionanotechnology Tutorials
All NAMD & VMD Tutorials
  

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

News

Team learns how membrane transporter moves
Charm++-Related Events at SC13
Extreme Computational Biology at SC13
Editors' Choice: Best use of HPC in life sciences
Rapid parameterization of small molecules
NAMD Paper Has 3000 Citations
Code cracks HIV capsid, opens drug possibilities
HIV-1 Capsid Structure Determined
Poliovirus Simulated on BlueGene/Q
Virus Structure Determined with Blue Waters
Fashioning NAMD: A History of Risk and Reward
Kale, Schulten Receive 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