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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made with VMD

Living cells employ an intricate network of biochemical processes for the conversion of solar energy or nutrients into energy-rich Adenosine Tri Phosphate (ATP) molecules. From bacteria to fungi, plants, and animals, ATP serves as the universal energy currency of life, fueling the processes cells need to survive and function. Over the course of a day, an individual will typically use the equivalent of his or her bodyweight in ATP; however, the human body carries only a small amount of the molecule at any one time. That means cells must constantly recycle or replenish the ATP molecules, relying on a highly efficient motor protein called ATP synthase to do the job. Given its ubiquitous role in photosynthesis and respiration, efficiency of the ATP synthase motor has been a focus of intense biochemical investigations over the past three decades, which included Boyer and Walker's Nobel Prize-winning contributions in 1997. Yet, connection between the Chemistry of ATP dissociation and Physics of ATP synthase motor-action remained elusive. A recent study based on molecular dynamics simulations with NAMD reveals the working principles of V-type ATP synthase in atomic resolution. Swiveling motions in the protein ring were captured together with rubber band-like elasticity of the motor's central stalk. This swiveling motion of the ring when paired with the stalk absorbs about 75 percent of the energy released during ATP hydrolysis, showcasing a molecular design that underlies the molecular motor's remarkable energy-conversion efficiency. More on ATPase here and 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