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.

The 2005 reference paper Scalable molecular dynamics with NAMD has over 1000 citations as of March 2010.

image size: 419.0KB
made with VMD

Voltage-gated ion channels, present in the membrane of excitable cells, control the ionic concentrations of the cellular environment by maintaining a potential difference of -100 mV between inside and outside of the cell membrane. Voltage-sensing occurs through distinct protein modules, known as voltage-sensor domains, four of which surround the main conduction pathway in potassium channels. Mutation of a certain amino acid on the voltage sensor domain turns these protein modules into cation channels, known as omega pores, which allow conduction of ions only when the main pathway is closed. Omega pores closely resemble the long-sought voltage-gated proton channels, which were recently identified to follow the same voltage-sensing mechanism as voltage-gated cation channels. In a recent report, researchers have visualized the twisted permeation pathway of the ions through omega pores using the molecular dynamics program NAMD. The simulations revealed a narrow constriction region lined by negatively charged amino acids, acting as a selectivity filter that prefers passage of positively charged ions through the pore. For more detail, see our potassium channel website .

Overview

Having Problems with NAMD?
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, NICS, or Texas

Training

In-Residence Training in Urbana
   (July 16-27, 2012) Apply by June 24.
Charm++ Workshop in Urbana (May 7-9, 2012)
Membrane Protein Modeling Workshop in Chicago (May 1-2, 2012)
"Hands-On" Workshop in Urbana (Feb 11-15, 2012)
Online Workshop on Simulating Membrane Channels (Nov 28-Dec 1, 2011)
"Hands-On" Workshop in Bremen (Oct 17-21, 2011)
Online Workshop on Simulating Membrane Channels (Aug 1-4, 2011)
In-Residence Training in Urbana (July 25-Aug 5, 2011)
"Hands-On" Workshop in Pittsburgh (May 16-20, 2011)
Charm++ Workshop in Urbana (April 18-20, 2011)
"Hands-On" Workshop in Atlanta (March 21-25, 2011)
GPU Programming Workshop in Urbana (Aug 7-8, 2010)
"Hands-On" Computational Biophysics Workshops
Older Workshops

Support

Announcements

NAMD 2.9 New Features
NAMD 2.9 (April 2012)
2011 User Survey Report
NAMD 2.8 New Features
NAMD 2.8 (May 2011)
NAMD 2.7 New Features
NAMD 2.7 (Oct 2010)
How to Cite NAMD
Previous Announcements

Documentation

Adaptive Biasing Force Website
Interactive Molecular Dynamics Tutorial
Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation

News

Hello Siri, Please Start My Experiment Now
Blue Waters Early Science System
Proteins Help DNA Replicate Past Damage
SC11: Scaling to 100 Million Atoms
Copper Folds Parkinson's Plaques
Mechanics of Membrane Proteins
Molecular Mystery of Blood Clotting
Alzheimer's Misfolding Simulated
When Cellular Bones Soften
Getting the Rabbit in the Hat
Insights Into Deafness
Molecular Machines Replicate and Repair DNA
Sound Science
Blueprint for the Affordable Genome
Mechanics of Hearing and Deafness
NAMD Paper Has 1000 Citations
Closing the Gaps
Inside the Swine Flu Virus
GPU Acceleration in Development
NCSA IACAT to Accelerate NAMD
Parkinson's, Alzheimer's Diseases
Knock, Knock, Who's There?
Step Up to the BAR Domain
Older News Items