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 4000 citations as of September 2014.

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: Step Up to the BAR Domain (Apr 2007)

BAR domain

PSC News Release: University of Utah chemist Gregory Voth and grad student Phil Blood are using PSC’s Cray XT3 to tackle a basic question of endocytosis—the life-sustaining process by which cells absorb material from outside the cell by bending their membrane to form a “vesicle” and engulf it. All animal cells depend on endocytosis, which involves various steps, but begins with curvature of the membrane.

BAR domains are a family of banana-shaped proteins shown to bind to cellular membrane as it curves. Experiments suggest that BAR domains mold their concave surface to a section of membrane and induce a corresponding curvature. Voth and Blood undertook molecular dynamics simulations to look more closely. With the XT3 they’ve been able to run efficiently, using software called NAMD, with as many as 1,024 processors. “The XT3 has been amazing,” says Blood. “We haven’t found a hard limit on scaling up the number of processors.

They used TeraGrid systems at SDSC, NCSA and University of Chicago/Argonne to construct a model and to explore how long a stretch of membrane they needed for curvature to occur. Their final simulations used the XT3 to include the protein with a 50-nanometer length of membrane—probably the longest patch of membrane ever simulated—for a total of 738,000 atoms. Their results, reported in Proceedings of the National Academy of Sciences (2006), show that the orientation of the BAR domain as it attaches to the membrane determines the degree of curvature.

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 Odense (Oct 12-16, 2015)
    Apply by September 1.
"Hands-On" Workshop in San Diego (Sept 21-25, 2015)
    Apply by August 20.
"Hands-On" Workshop in Berkeley (August 3-7, 2015)
    Apply by July 15.
"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)
"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 2.11 New Features
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

Documentation

NAMD 2.10 User's Guide
   
  (also 728k HTML or 1.1M PDF)
NAMD 2.10 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

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
TCBG Papers and Presentations at SC14
Charm++-Related Events at SC14
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
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