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: Graphene Nanopore Sensor (Nov 2014)

DNA graphene

image size: 287.1KB
made with VMD

Threading DNA through a nanometer-size pore, so called nanopores, drilled into an ultrathin graphene membrane is a promising approach to build nanobiosensors for sequencing the human genome. Graphene nanopores can detect translocating DNA by recording concomitant flow of charged ions through the pore (see December 2011 highlight). As reported in the December 2013 highlight, graphene, which is an electrical conductor, offers a new way of sensing DNA molecules by monitoring sheet currents along the graphene membrane. DNA is a highly extensible molecule and upon mechanical manipulation can change its structure from a canonical helical conformation to a linear zipper-like conformation. A new study, which combines classical molecular dynamics simulations using NAMD with quantum mechanical simulations, suggests that sheet currents, in graphene membranes, can be used to detect conformation and sequence of a DNA molecule passing through the nanopore. This new research will guide the development of graphene-based nanosensors for DNA detection. More information can be found on our graphene nanopore 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

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

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