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 5000 citations as of October 2015.

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: Small Proteins into the Cell Membrane (July 2015)

YidC : MDFF vs crystal

image size: 901.7KB
made with VMD

Synthesis and placement of new proteins in a living cell poses a challenge for the cellular machinery, in particular in case of so-called membrane proteins. Starting with nothing more than a sequence of DNA, the cell has to translate the genetic code, stitch together the constituent amino acids, and then place the newly made protein where its function is needed, namely the cell membrane. To meet the challenge the cell employs a molecular machine for the synthesis of proteins, the ribosome (see the Dec. 2009 highlight on Managing the Protein Assembly Line ), as well as special proteins that translocate newly synthesized proteins out of the machine into the cell membrane (see the Feb. 2011 highlight on Placing New Proteins ). Depending on the complexity of the membrane protein insertion, different protein systems are used for the translocation, in most cases the systems involving complexes of several, even many, proteins. Now however, the structure and function of the simplest translocating protein system has been solved, which actually is made of only a single protein, called YidC. Despite its simplicity, structure determination of YidC was difficult, taking three decades. Successful structure determination was recently reported here, and involved the combination of cryo-electron microscopy, mutational experiments and computer simulations, the latter using NAMD, VMD and MDFF. The structure that was discovered shows a distinctive arrangement of five trans-membrane helices and reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-membrane lipid interface. The quality of this atomic model is validated by its close agreement with a recently published crystal structure of E. Coli YidC (here). More on our protein translocation 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

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)
"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 2.11 (Dec 2015)
NAMD 2.11b2 (Dec 2015)
NAMD 2.11b1 (Nov 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

Documentation

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

News

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
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