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: Oil and Water Split DNA (Dec 2007)

DNA pulling through octane

image size: 162.1KB
movie: 4.2MB
made with VMD

Ever since the 1953 discovery of DNA's double helix structure researchers wondered how the double strands are separated so that genetic information stored inside the helix can be delivered from generation to generation. A class of proteins known to achieve this separation are DNA helicases (see Sept 2006 highlight), molecular motors that operate at a fork where a double stranded DNA separates into two single stranded DNAs. Helicases translocate along one of the single stranded DNAs, pushing forcefully into the fork to split the double stranded DNA apart further. Helicases seem to work, though, both through force and through persuasion, exposing to the double stranded DNA a surface that is apparently conducive for strand separation. This property suggests itself on account of the fact that many of the amino acid side groups at the relevant surface are highly conserved among species or evolved from species to species through pairwise mutation. But what chemical strategy evolution had in mind in molding the surface was not realized. Recently, however, researchers seeking artificial means of splitting double stranded DNA apart might have found a key clue. They pulled double stranded DNA at one of its single strands by means of an atomic force microscope from DNA's native salt water environment into a so-called non-polar solvent. The force - distance curve measured suggested that the DNA actually split apart, but there existed no direct experimental means of viewing the splitting. The researchers employed instead molecular dynamics simulations, using NAMD, that indeed clearly revealed the splitting of the DNA strands at a water - oil (octane) interface as reported in a recent publication. The study suggests how helicases achieve the splitting of DNA strands, namely by altering the local environment of DNA from water-like (hydrophilic) to oil-like (hydrophobic). More information 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