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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Computer simulations of the biomolecular processes in human cells guide better understanding of health and disease as well as development of dietary supplements and pharmacological treatments. Such simulations are extremely demanding and, in fact, all too often still limited by technological feasibility. However, technological advances are being brought to bear on computer simulations in biomedicine through highly dedicated biomedical engineers, who have often speerheaded uses of new computer technologies such that they became available in biomedicine much sooner than in other fields. A case in point is solid state disk (SSD) technology that can serve as extremely fast and large computer memory. Conventional RAM (random access memory) is fast, but limited in size due to cost; the well known hard disks (HDs) can hold large data sets at an affordable price, but are slow. The new SSDs are in the middle ground, faster than HDs, slower than RAM, offering large data storage at an affordable price. Modern uses of SSDs in smart phones and tablets attest to the usefulness of SSDs. The biomolecular visualization and analysis software VMD in its next release (VMD 1.9.1) makes the power of SSDs as a huge, yet fast storage medium available to biomedical researchers. As reported, this will allow them to view and analyze through VMD on the fly Gigabytes-to-Terabytes of simulation data, that are being raked into a computer at the rate of up to 4 Gigabytes per second (one high definition video of a long movie per second!). For more on this and other revolutionary features of VMD 1.9.1 see our VMD web site.

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