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 processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. 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: Diet and DNA (Sept 2011)
The genes of organisms, like plants and animals, offer the blueprint, not only to build the organism anew from a seed or fertilized egg cell, but also to adapt the living organism to its habitat and life experience. For example, a type of tree growing in an arid or wet region will adapt expression of its genes for root growth optimal to circumstances. A child living on a scarce or abundant diet or with little or much physical activity will adapt body growth accordingly. The adaptation of an individual's gene expression is the subject of epigenetics. One control element in epigenetics is that cytosine bases of an organism's DNA become methylated at the 5-position in a chemical reaction in which the hydrogen atom is replaced by a methyl group (CH3). DNA methylation patterns depend on an organism's individual history; aberrant methylation patterns can be the cause of diseases, for example, of certain cancers. It is known that the proteins involved in gene expression can recognize methylated sites of DNA and, thereby, direct gene expression; DNA methylation also affects the packing of DNA in the chromosomes. However, methylation may also affect gene expression directly; experiment and computational modeling with NAMD suggest now an intriguing third way how methylation can regulate gene expression. Methylation is shown, as reported recently, to make it more difficult to separate the two strands of DNA, as is necessary during gene expression. An earlier experimental-computational study had revealed already that methylated DNA can pass narrow synthetic nanopores more readily than unmethylated DNA can (see the Feb 2009 highlight). The two experimental-computational findings advance our understanding of methylation-based epigenetics and of how our body adapts to our life style and diet. More on our methylated DNA website.
Overview
Having Problems with NAMD?
Why NAMD? (in pictures)
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 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 (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
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
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