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.

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Breaking News

NAMD will be used for groundbreaking coronavirus simulations that will run on the Frontera supercomputer at TACC. The Amaro Lab of UC San Diego is working to build the first complete all-atom model of the SARS-COV-2 coronavirus envelope in order to investigate how the virus interacts with receptors within the host cell membrane. The coronavirus model is anticipated to contain 200 million atoms. The simulations will run on up to 4,000 nodes or about 250,000 processing cores of Frontera.

coronavirus

Other Spotlights 

Spotlight: Ten Years of NAMD (Oct 2005)

IMD user with haptic device

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Olga Svinarski and VMD

It was 1995 when NAMD was introduced (Nelson et al.) as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. In 1999 a major improvement was accomplished in NAMD 2 (Kalé et al.), scaling to 200 processors at the time due to the efforts and software of the Parallel Programming Lab. NAMD has since matured, adding many features and scaling to thousands of processors, garnering accolades and users in the process. This progress is now collected in a NAMD review paper that presents, in a manner accessible to the novice researcher, the concepts and algorithms behind NAMD, features for steered and interactive MD and for free energy calculation, the elements of the NAMD design that enable parallel scaling, performance comparisons of a variety of platforms, and advice for productive use of NAMD on modern research projects. Case studies ranging from the typical to the elaborate demonstrate the capabilities and flexibility of NAMD. This new reference provides an excellent foundation for working through the extensive NAMD tutorials, either on your own or at a hands-on workshop.

Overview

Why NAMD? (in pictures)
How to Cite NAMD
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

NAMD Developer Workshop in Urbana (August 19-20, 2019)
PRACE School on HPC for Life Sciences (June 10-13, 2019)
"Hands-On" Workshop in Pittsburgh (May 13-17, 2019)
Charm++ Workshop in Urbana (May 1-2, 2019)
Enhanced Sampling and Free-Energy Workshop (Sept 10-14, 2018)
NAMD Developer Workshop in Urbana (June 11-12, 2018)
"Hands-On" Workshop in Pittsburgh (May 21-25, 2018)
"Hands-On" QM/MM Simulation Workshop (April 5-7, 2018)
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 2.14b2 Release (June 2020)
NAMD 2.14b1 Release (May 2020)
NAMD 2.13 Release (Nov 2018)
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
Previous Announcements

Documentation

NAMD 2.14b2 User's Guide
   
  (also 5.1M HTML or 5.5M PDF)
NAMD 2.14b2 Release Notes
Running Charm++ Programs (including NAMD)
Running GPU-Accelerated NAMD (from NVIDIA)
Introductory NAMD Tutorials
All NAMD & VMD Tutorials
  

Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation

News

Coronavirus Simulations by U. Delaware Team
Coronavirus Simulations on Frontera Supercomputer
Breakthrough Flu Simulations
Oak Ridge Exascale Readiness Program
Prepping for Next-Generation Cray at NERSC
Supercomputing HIV-1 Replication
How GPUs help in the fight against staph infections
Computational Microscope Gets Subatomic Resolution
Opening New Frontiers in the Battle Against HIV/AIDS
HIV Capsid Interacting with Environment
Assembling Life's Molecular Motor
Older News Items