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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Other Spotlights 

Spotlight: NAMD 2.10 Advances Simulations Large and Small (Jan 2015)

GlpT protein embedded in membrane

image size: 11.9MB
made with VMD

The 2.10 release of the molecular dynamics program NAMD includes numerous enhancements to support simulations of massive supramolecular assemblies such as the HIV capsid (see highlight Elusive HIV-1 Capsid). A single such simulation of a hundred million atoms or more can utilize the tens of thousands of processors of petascale supercomputers thanks to recent advances in computational methodology reported here. Equally if not more significant, however, are advances in NAMD's implementation of multiple copy algorithms for enhanced sampling of smaller molecular systems as reported here. These algorithms have already allowed researchers studying the molecular machinery of living cells to reveal for the first time with NAMD mechanisms operating on timescales of milliseconds or longer, including the rotary action of the ubiquitous energy conversion complex ATP synthase and the inward to outward opening transition of the membrane transporter protein GlpT, shown in the accompanying animation. NAMD 2.10 also introduces multilevel summation, reported here, a major algorithmic advance enabling efficient long-range electrostatics for non-periodic and semi-periodic simulations. More on new features in the 2.10 release of NAMD can be found here.

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

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)
Enhanced Sampling and Free-Energy Workshop (Sept 25-29, 2017)
"Hands-On" Workshop in Pittsburgh (May 30-June 2, 2017)
NAMD Developer Workshop in Chicago (May 22-23, 2017)
"Hands-On" Workshop in Urbana (April 17-21, 2017)
PRACE School on HPC for Life Sciences (April 10-13, 2017)
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 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 2.13 User's Guide
   
  (also 4.9M HTML or 5.3M PDF)
NAMD 2.13 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

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