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 1000 citations as of March 2010.
Spotlight: Large Protein Folded Computationally (July 2012)
Proteins are the biological workhorses in living cells. For example, they respond to external signals arriving at the cell surface or transport cargo, much larger than themselves, from one place to another in the cell. However, before a protein can carry out his job, it must first assume the proper shape. Proteins are long polymers of twenty different amino acids linked in a linear sequence; the latter is particular for each protein. It is still a mystery how a protein folds into the proper shape based on its sequence. Scientists hope that one day they can "watch" this folding process for any given protein. The dream has been realized, at least partially, through the use of computer simulation. After tackling the protein-folding problem already computationally for two small proteins (see May 2008 highlight and Nov 2009 highlight), researchers have now successfully visualized the complete folding process of a relatively large protein, the so-called λ-repessor (see movie, 7.8 MB). In fact, it is one of the largest proteins folded to date using a computer. As reported recently, simulations carried out with the program NAMD, as well as simulations carried out on a special purpose supercomputer, Anton, achieved to follow λ-repessor's folding movement for more than 0.0001 seconds, long enough to observe the protein assume its proper shape. More information is available on our protein folding 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
GPU Programming Workshop in Urbana
(Aug 2-4, 2013) Apply by July 15.
"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)
Online Workshop on Simulating Membrane Channels (Nov 28-Dec 1, 2011)
"Hands-On" Workshop in Bremen
(Oct 17-21, 2011)
Online Workshop on Simulating Membrane Channels (Aug 1-4, 2011)
In-Residence Training in Urbana
(July 25-Aug 5, 2011)
"Hands-On" Workshop in Pittsburgh (May 16-20, 2011)
Charm++ Workshop in Urbana (April 18-20, 2011)
"Hands-On" Workshop in Atlanta (March 21-25, 2011)
GPU Programming Workshop in Urbana (Aug 7-8, 2010)
"Hands-On" Computational Biophysics Workshops
Older Workshops
Support
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
Adaptive Biasing Force Website
Interactive Molecular Dynamics Tutorial
Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation
News
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
