NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, 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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Photosynthetic organisms have been optimized by over two billion years of evolution into energy-harvesting machines that surpass the efficiency of man-made solar devices. Employing a network of hundreds of proteins, these organisms transform energy from the incident sunlight into ATP molecules - the universal fuel for sustaining cellular activities. A key step in the conversion of solar energy into ATP involves shuttling of negative charges or electrons between widely separated sites on the cell membrane. This membrane-wide charge transportation is accomplished by the cytochrome c family of proteins. Cytochrome c finds and docks to an electron donor protein, accepts the electron and unbinds as a result of it, and afterwards finds an electron acceptor protein, docks to it to deliver the electron and unbinds to repeat the sequence. Given its ubiquitous role in photosynthesis and respiration, the recognition, binding and unbinding mechanism of cytochrome c have been a focus of intense biochemical investigations over the past three decades. However, little is deciphered on the details of cytochrome c activity. A recent study based on molecular dynamics simulations with NAMD reveals the working principles of cytochrome c in atomic resolution. The calculations suggest that electrostatic forces drive the cytochrome c binding, and enable membrane-wide electron transfer. More about the cytochrome c protein 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

NAMD Developer Workshop in Urbana (August 19-20, 2019)
PRACE School on HPC for Life Sciences (June 10-13, 2019)
"Hands-On" Workshop in Pittsburgh (May 13-17, 2019)
Charm++ Workshop in Urbana (May 1-2, 2019)
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)
Older "Hands-On" Workshops

Support

Announcements

Documentation

Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation

News

Sparing healthy microbes while using a novel antibiotic
AMBER force field use in NAMD for large scale simulation
NAMD GPU-resident benchmarks available
NAMD and VMD share in COVID-19 Gordon Bell Special Prize
NAMD reference paper published online
Coronavirus Simulations by U. Delaware Team
Coronavirus Simulations on Frontera Supercomputer
Breakthrough Flu Simulations
Oak Ridge Exascale Readiness Program
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