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 3.0 New Features - webpage is posted |
| NAMD GPU-resident benchmarks - results and data sets with GPU-optimized configuration posted |
| NAMD 3.0b6 Release - fixes important bugs from last two beta releases |
| NAMD 2.15 ALPHA Release providing GPU-offload support for Intel GPU Max Series. This source code release available on the download page includes SYCL code that can be built using the Intel oneAPI toolkits. Following the download link reveals a page with detailed build instructions. |
Spotlight: VMD 1.9.3 Brings Simulations Into Focus (March 2017)
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made with VMD
The latest release of VMD brings many advances that help researchers prepare, analyze, and visualize molecular simulations. The new QwikMD plugin streamlines key simulation preparation and analysis tasks, and guides users in the creation of reusable simulation workflows and protocols. VMD now includes several advanced features for parallel analysis and visualization of cellular-scale simulations, as reported here, and here. VMD 1.9.3 strengthens collaboration between experimental and computational biologists by supporting a broader range of experimental density map image formats, such as those used in cryo-electron tomography. Many updated plugins are included in VMD 1.9.3, including tools for analysis of free energy perturbation simulations, MDFF hybrid structure fitting, ffTK force field parameterization, and normal mode analysis. VMD 1.9.3 adds support for new hardware and operating system platforms including IBM OpenPOWER (ORNL Summit), a variety of GPU-accelerated ARM SoCs, the Amazon AWS EC2 cloud, and most recently, the Intel Xeon Phi Knight's Landing many-core CPU (TACC Stampede 2, Argonne Theta). The VMD 1.9.3 release adds stunning graphics produced using interactive ray tracing using the latest multi-core CPUs and GPU accelerators, enabling 360-degree panoramic movie rendering for VR headsets, as reported here, and here. Interactive ray tracing makes the task of getting a molecular image "just right" much easier than ever before; it also enables rendering of spectacular movies for communication of scientific results. A VR movie rendering tutorial assists users with the steps required in rendering and encoding VR movies for upload to YouTube for display using VR headsets such as Google Cardboard, Oculus Rift, and GearVR. More details about VMD 1.9.3 features 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
Mailing List Issues for Yahoo.com Addresses
Announcements
NAMD 3.0b6 Release (Feb 2024)
NAMD 3.0 New Features (Feb 2024)
NAMD 2.14 Bug Fixes (Apr 2022)
NAMD 2.14 Release (Aug 2020)
NAMD 2.14 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
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
