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.

The 2005 reference paper Scalable molecular dynamics with NAMD has over 6,000 citations as of October 2016.

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

NAMD Powers Molecules by Theodore Gray App for iPhone and iPad

Multilevel Summation Method for Electrostatic Force Evaluation, JCTC, 2014.

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Other Spotlights 

Spotlight: Epigenetic Key (Jan 2012)

MBD protein binds to mDNA

image size: 85.6KB
made with VMD

Genes encoded in DNA sequence give a complete set of instructions for the development of a new organism. However, an organism, like the human body, develops also over a life time adapting to environment and experience, for example to diet and exercise. Recently, researchers found that such factors act through so-called epigenetic mechanisms that alter an organism's development without altering DNA sequence. One such mechanism involves DNA methylation, a chemical modification of one of the four bases of DNA, cytosine, that replaces a hydrogen atom with a methyl group. There are several ways that DNA methylation exerts its biological function, bringing about a long-time adaptation of an organism to its environment, in some cases even across generations. Our previous experimental and computational studies (see Sep 2011 and Feb 2009 highlights) indicated that methylation changes mechanical properties of DNA which can affect gene expression. DNA methylation can also inhibit gene expression by impeding proteins that control the translation of DNA sequence into protein synthesis. One mechanism involves DNA methylation sites recruiting genetic control proteins that inhibit DNA expression through their local presence. In a recent study, computational biologists performed MD simulations with NAMD along with quantum chemistry calculations to determine recognition of methylated DNA by proteins. The simulations revealed how a certain genetic control protein, called methyl-CpG binding domain protein, acts in tandem with methylated DNA like a key and a lock, methylated DNA and protein perfectly matching each other. More details can be found on our methylated DNA website.


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Publications and Citations
Credits and Development Team


Read the License
Download NAMD Binaries (also VMD)
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Run at NCSA, SDSC, NICS, or Texas


"Hands-On" Workshop in San Francisco (Dec 12-16, 2016)
    Apply by November 18.
"Hands-On" Workshop in Atlanta (Nov 14-18, 2016)
"Hands-On" Workshop in Urbana (Oct 17-21, 2016)
"Hands-On" Workshop in Jülich (Aug 15-19, 2016)
"Hands-On" Workshop in Pittsburgh (June 6-10, 2016)
NAMD Developer Workshop in Chicago (May 26-27, 2016)
Charm++ Workshop in Urbana (April 19-20, 2016)
"Hands-On" Workshop in Odense (Oct 12-16, 2015)
"Hands-On" Workshop in San Diego (Sept 21-25, 2015)
"Hands-On" Workshop in Okazaki (Sept 9-11, 2015)
"Hands-On" Workshop in Berkeley (August 3-7, 2015)
"Hands-On" Workshop in Pittsburgh (June 1-5, 2015)
Charm++ Workshop in Urbana (May 7-8, 2015)
"Hands-On" Workshop in Urbana (April 6-10, 2015)
"Hands-On" Workshop in Atlanta (Nov 3-7, 2014)
"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)
Older "Hands-On" Workshops


Having Problems with NAMD?

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

Mailing List Issues for Addresses


NAMD 2.12 New Features
2016 User Survey Report
NAMD 2.11 New Features
NAMD 2.11 (Dec 2015)
NAMD 2.10 New Features
NAMD 2.10 (Dec 2014)
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


NAMD 2.11 User's Guide
  (also 728k HTML or 1.1M PDF)
NAMD 2.11 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


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
Key Component in Bacterial Decisions
TCBG Papers and Presentations at SC15
Charm++-Related Events at SC15
TCBG Reaches Milestone 40th Workshop
NAMD Paper Has 5000 Citations
Transport Cycle in Atomic Detail
Atomic Model of Immature Retrovirus
ANL Supercomputer Early Science Program
Cellulosomes: One of Life's Strongest Bonds
ORNL Supercomputer Readiness Program
Solving Puzzle-Like Bond for Biofuels
Real Science Using Stampede's Xeon Phi
App Puts Chemistry at the Tips of Users' Fingers
NAMD Powers Molecules by Theodore Gray
Big Ten Network "Computing a Virus" Feature
NAMD Paper Has 4000 Citations
Bolstering Extreme Scale Computational Biology
CUDA Achievment Award for Fighting HIV
Team learns how membrane transporter moves
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
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
Older News Items