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.

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: HIV, Cells, and Deception (Nov 2015)

HIV-1 Capsid

image size: 283.9KB
made with VMD

When human immundeficiency virus (HIV) infects a human cell, it releases into the interior of the cell its capsid (made of about 1,300 identical so-called CA proteins), a closed, stable container that protects the viral genetic material (see also June 2013 highlight Elusive HIV-1 Capsid and August 2015 highlight Anatomy of a Dormant Killer). Once in the cell ― while avoiding detection by cellular proteins ― the capsid deceives the cell and directs the cell machinery to transport it to the nucleus. The human-cell protein Cyclophilin A (CypA) is thereby exploited to act against the cell's well being and to assist the HIV infection by getting the capsid to access the cell nucleus; this results in a delicate choreography accomplished by escaping anti-viral proteins in the cell and deceiving transport proteins at the nucleus, all of which contain a CypA domain that interacts directly with the capsid. Despite the availability of the crystal structure of the complex of CypA and CA proteins determined nearly 20 years ago, the mechanism by which CypA assists the capsid has been unclear due to the lack of information on CypA in complex with not one CA protein, but the entire capsid. In collaboration with experimental groups, computational biologist have shown in a recent report that the effects of CypA on the capsid are not only structural, but also dynamical. Thus, new therapeutic strategies may be envisioned through modulation of the dynamics of the capsid by small-molecule (drug) compounds that inhibit the binding of CypA to the capsid. More information is available on our retrovirus website and in a YouTube video.

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 - Git access now available
Run at NCSA, SDSC, NICS, or Texas

Training

Enhanced Sampling and Free-Energy Workshop (Sept 25-29, 2017)
    Held in Urbana, IL. Apply by August 11.
"Hands-On" Workshop in Pittsburgh (May 30-June 2, 2017)
NAMD Developer Workshop in Chicago (May 22-23, 2017)
Charm++ Workshop in Urbana (April 17-19, 2017)
"Hands-On" Workshop in Urbana (April 17-21, 2017)
PRACE School on HPC for Life Sciences (April 10-13, 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)
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 2.13 New Features
One-click NAMD/VMD in the cloud
QM/MM Interface to MOPAC and ORCA
QwikMD GUI Released in VMD 1.9.3
NAMD 2.12 New Features
NAMD 2.12 (Dec 2016)
2016 User Survey Report
NAMD 2.11 New Features
NAMD 2.11 (Dec 2015)
How to Cite NAMD
Previous Announcements

Documentation

NAMD 2.12 User's Guide
   
  (also 773k HTML or 1.1M PDF)
NAMD 2.12 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

HIV Capsid Interacting with Environment
Assembling Life's Molecular Motor
Roux Early Science Project on ANL Aurora
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
Older News Items