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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Biofuels are a well-known alternative to the largely used fossil-derived fuels, however the competition with food production is an ethical dilemma. Fortunately a solution is offered by second-generation biofuels, which can be produced from agricultural waste, or more specifically, from plant cell wall polysaccharides. Using the strategy of microorganisms, several enzymes are employed in the production of this advanced biofuel. However the biofuel industry faces problems such as the loss of efficiency of the enzymes that arises over time due to intermittent high concentration of non-suitable substrates. Simulations can guide biochemical experiments aimed at investigating the mechanism that makes the enzymes vulnerable to such substrates, helping the development of more efficient and, thereby, less costly enzymes. A recent study, based on molecular modeling with NAMD, reported that reduction of efficiency in an important enzyme, know as Man5B, is associated with a loss of the enzyme's flexibility. Molecular dynamis simulations showed that a poor substrate slows down a crucial opening and closing movement of the enzyme's catalytic cleft while a good substrate keeps the movement almost intact. The insight is of crucial importance since it suggests mutations to enzymes presently employed in second-generation biofuel production that need to be replaced less often and, thereby, rendering the production more cost-effective. Read more on our biofuels website.

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