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.

Search all NAMD resources:

Other Spotlights 

Spotlight: xMDFF Enhances X-Ray Structures (Aug 2014)

xMDFF

image size: 151.9KB
made with VMD

For many, the word 'X-ray' conjures up the images of white bones on black backgrounds hanging on the wall of a doctor's office. However, X-rays have played another important role for the past 100 years through their use in the determination of chemical structures at atomic level detail, starting with the first ever structure of table salt in 1924. Since then, the diffraction properties of X-rays, when shone on a crystal, have been used to solve increasingly large and complex structures including those of biological macromolecules found inside living cells. X-ray crystallography has become the most versatile and dominant technique for determining atomic structures of biomolecules, but despite its strengths, X-ray crystallography struggles in the case of large or flexible structures as well as in the case of membrane proteins, either of which diffract only at low resolutions. Because solving structures from low-resolution data is a difficult, time-consuming process, such data sets are often discarded. To face the challenges posed by low-resolution, new methods, such as xMDFF (Molecular Dynamics Flexible Fitting for X-ray Crystallography) described here, are being developed. xMDFF extends the popular MDFF software originally created for determining atomic-resolution structures from cryo-electron microscopy density maps (see the previous highlights Seeing Molecular Machines in Action, Open Sesame, Placing New Proteins, and Elusive HIV-1 Capsid). xMDFF provides a relatively easy solution to the difficult process of refining structures from low-resolution data. The method has been successfully applied to experimental data as described in a recent article where xMDFF refinement is explained in detail and its use is demonstrated. Together with electrophysiology experiments, xMDFF was also used to validate the first all-atom structure of the voltage sensing protein Ci-VSP, as also recently reported. More on our MDFF 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

"Hands-On" Workshop in Lake Tahoe (August 3-7, 2015)
    Apply by July 15.
"Hands-On" Workshop in Pittsburgh (June 1-5, 2015)
    Apply by May 4.
Charm++ Workshop in Urbana (May 7-8, 2015)
    Register by May 1 or attend via webcast.
"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