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.

QwikMD - integrative molecular dynamics toolkit for novices and experts, Scientific Reports, 2016.

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Other Spotlights 

Spotlight: Modeling a Crucial Membrane Channel (Feb 2007)

image size: 311.9KB
made with VMD and Tachyon

Bacteria employ membrane proteins as crucial safety valves that release water and small solutes under challenging osmotic conditions (see the May 2006 highlight, "Electrical Safety Valve" and the Nov 2004 highlight, "Japanese Lantern Protein"). There are valves for balancing small pressure differences between the inside and outside of bacterial cells, that open and close readily, but there are also ones for protection against large pressure differences as a safety measure of last resort. The valves for balancing small pressure differences, like the one shown in the figure, include a filter that presumably keeps the most valuable molecules inside the cell interior, though this is not understood yet in detail. To reveal the function of such channels a combination of X-ray crystallography, physiological measurements, and molecular dynamics simulations using NAMD has been employed. Crystallography, in a prior study, captured the channel in a half-way open state. Now a team of physiologists and modelers reported the details on valve opening and closing. The experiments, using a pipette small enough to measure currents from a single channel, MscS, along with the simulations revealed that the channel conducts both positive and negative ions when subjected to tension and voltage. The unprecedented comparison of experimental and computational results open a new era of quantitative cell biology that borrows successful research strategies from physics (more on our MscS 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 Urbana - Topics TBD (Feb 20-24, 2017)
"Hands-On" Workshop in San Francisco (Dec 12-16, 2016)
"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

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 2.12 New Features
NAMD 2.1b11 (Nov 2016)
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

Documentation

NAMD 2.12b1 User's Guide
   
  (also 774k HTML or 1.1M PDF)
NAMD 2.12b1 Release Notes
Running Charm++ Programs (including NAMD)
Running GPU-Accelerated NAMD (from NVIDIA)
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

Membrane Channel Made of DNA Origami
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