NAMD, recipient of a 2002 Gordon Bell 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 processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. 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.
NAMD reference paper: Scalable molecular dynamics with NAMD.
Spotlight: Molecular Obstacle Course (Jan 2008)
Biological cells protect their interior through their cellular membranes, yet rely on import of nutrients. They have evolved for this import fast conduction channels that include reliable checkpoints distinguishing desirable and undesirable compounds. A checkpoint puts up a veritable obstacle course that only the right compounds can pass quickly. Understanding the channel design is difficult due to lack of detailed experimental data on nutrient dynamics. Presently, the most detailed information comes from viewing channel dynamics computationally, starting from static crystallographic structures. A recent study investigated how glycerols, small nutrient molecules needed by some bacteria, pass through checkpoints realized through the membrane protein aquaporin (see also highlights Gas Molecules Commute into Cell - Mar 2007, Aquaporin and the Cambridge Five - Oct 2006, Cellular Faucets - Feb 2006). Aquaporin furnishes four parallel channels that were monitored computationally using NAMD and a novel algorithm that explores the channel energetics quickly enough to be methodologicaly feasible on today's computers. The results show how the physical characteristics of glycerol, for example the molecule's ability to form so-called hydrogen bonds, its electrical dipole moments, its diffusive mobility and intrinsic flexibility are probed along the channel, discriminating glycerol from other molecules. More on computational investigations of aquaporin here.
Overview
Why NAMD? (in pictures)
Steered Molecular Dynamics
Interactive Molecular Dynamics
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
Run at NCSA, SDSC, PSC, Indiana, or Texas
NAMD in Scienomics Software
Training
Charm++ Workshop (May 1-3, 2008)
Cluster-Building Workshop (11/30-12/1, 2006)
Cluster-Building Workshops (3/16-17 & 4/20-21, 2006)
Frankfurt Hands-On Workshop (March 20-23, 2006)
Cluster-Building Workshops (9/22-23 & 11/10-11, 2005)
Older Workshops
Support
Contact the DevelopersAnnouncements
NAMD 2.6 (August 2006)
2005 User Survey Report
NAMD 2.5 (Sept. 2003)
NAMD 2.4 (Mar. 2002)
How to Cite NAMD
Previous Announcements
Documentation
Adaptive Biasing Force Website
Adaptive Biasing Force Calculations
Alchemical Free Energy Perturbation
Interactive Molecular Dynamics Tutorial
Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation
News
GPU Acceleration in Development
NCSA IACAT to Accelerate NAMD
Buckyball Bowling in Reno
TCBG Software at SC07
Parkinson's, Alzheimer's Diseases
Knock, Knock, Who's There?
Step Up to the BAR Domain
Protein Wranglers
Virus Simulated on SGI Altix
NAMD-G Paper Available
Managing Workflow with NAMD-G
Enzyme Antics
All in Your Brain
SPICE Wins HPC Analytics Challenge
Understanding the Protein Lock
Mechanosensitive Ion Channels
NAMD Wins Gordon Bell Award
Older News Items