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.
Breaking News
| NAMD and VMD are part of the team winning the 2020 ACM Gordon Bell Special Prize for high performance computing-based COVID-19 research, for the paper AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics, presented at Supercomputing 2020, Nov 18, 2020. |
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| University of Illinois has established a oneAPI academic Center of Excellence, using oneAPI to bring its cross-architecture single programming model to NAMD in order to address exascale computing challenges of COVID-19. |
| NAMD is able to achieve 9x throughput with version 3.0alpha running on NVIDIA A100 GPUs. Details available on the NVIDIA developer blog. |
| The new NAMD reference paper has been published online. The paper provides an overview of the many features available in NAMD, its scalability on CPU and GPU platforms on system sizes of up to a billion atoms, and the recent performance enhancements for GPU accelerators. |
Spotlight: Computing the Bacterial Brain (March 2016)
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made with VMD
Motile bacteria position themselves within their habitats optimally, seeking proximity to favorable growth conditions while avoiding unfavorable ones. Cues used for this placement come in the form of small chemicals, so-called attractors and repellants, as well as physical factors such as favorable visible light and unfavorable UV radiation. To balance such a broad range of factors, bacteria monitor their environments and respond by way of a fundamental sensory capability known as chemotaxis. Chemotactic responses in bacteria involve large complexes of sensory proteins, known as chemosensory arrays, that process the information obtained from the bacteria's habitat to determine its swimming pattern. In this sense, the chemosensory array functions as a bacterial brain, transforming sensory input into motile output. Despite great strides in the understanding of how the chemosensory array's constituent proteins fit and work together, a high-resolution description of the kind needed to explore in detail the molecular mechanisms underlying sensory signal transduction within the array has remained elusive. A new study, utilizing cryo-electron microscopy and molecular dynamics simulations with NAMD, reports the highest resolution images yet of the bacterial brain's molecular anatomy. Using computational techniques, structural data from X-ray crystallography and electron microscopy are compared to derive an atomically resolved model of the chemosensory array's extended molecular structure that involves millions of atoms. Subsequent simulations of the model revealed a novel conformational change in a key sensory protein, that is interpreted as a key signaling event in the translation of chemosensory information into swimming pattern. More details on this work can be found in a recent news release as well as on our bacterial chemotaxis 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
Mailing List Issues for Yahoo.com Addresses
Announcements
NAMD 2.14 Bug Fixes (Apr 2022)
NAMD 2.14 Release (Aug 2020)
NAMD 2.14 New Features
NAMD 2.13 Release (Nov 2018)
NAMD 2.13 New Features
One-click NAMD/VMD in the cloud
QM/MM Interface to MOPAC and ORCA
QwikMD GUI Released in VMD 1.9.3
Previous Announcements
Documentation
Related Codes, Scripts, and Examples
NAMD Wiki (Recent Changes)
Older Documentation
News
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
