NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, 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 3.0 New Features - webpage is posted

NAMD GPU-resident benchmarks - results and data sets with GPU-optimized configuration posted

NAMD 3.0b6 Release - fixes important bugs from last two beta releases

Other Spotlights 

Spotlight: Traffic Control Nanodevice (March 2014)

Structural model of nuclear pore complex.

image size: 579.0KB
made with VMD

Nanoengineers building nanodevices achieve technological solutions at scales of 100 nanometers or 0.0001 mm. Nanoengineering is a brand new human technology, just a few decades old. In living cells, nanoengineering solutions are actually a few billion years old and therefore much more intricate. An impressive example is the nuclear pore, hundreds to thousands of which dot the nuclear membrane that separates in eukaryotic cells the genome and its molecular control factors from the cytoplasm of the cell. Only since very recently could cell biologists begin to resolve the molecular architecture of the nuclear pore. Given the pore's many-fold functions, like letting small molecules pass easily, but larger ones only as cargoes of special proteins, the transport factors, or adapting the pore size when large cargoes need to pass, the architecture of the nuclear pore is complex, involving an assembly of hundreds of proteins. The interior of the pore is filled with 600 amino acid-long "finger" proteins tethered at the periphery. The finger proteins are largely disordered such that experimental methods lack resolving power and computational modeling is needed to figure out their dynamic arrangement and traffic control function, but such modeling was largely unfeasible; only a small fraction of the nuclear pore volume could be covered computationally. The advent of petascale computing increased the size-scale of biomolecular simulations hundred-fold and a recent report employing the programs NAMD and VMD took advantage of the new generation of computers, simulating the dynamic, disordered arrangement of nuclear pore proteins. The simulations, still at an early stage, suggest a detailed, atomic level picture of the nuclear pore interior together with an explanation of molecular traffic control. More on our nuclear pore website.

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 3.0b6 Release (Feb 2024)
NAMD 3.0 New Features (Feb 2024)
NAMD 2.14 Bug Fixes (Apr 2022)
NAMD 2.14 Release (Aug 2020)
NAMD 2.14 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 2.14 User's Guide
  
   (also 5.1M HTML or 5.5M PDF)
NAMD 2.14 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

AMBER force field use in NAMD for large scale simulation
NAMD GPU-resident benchmarks available
NAMD and VMD share in COVID-19 Gordon Bell Special Prize
NAMD reference paper published online
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