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 3.0.2 Release - Point release 3.0.2 fixes critical bugs in the Colvars module that affect not only NAMD 3.0 and 3.0.1, but also earlier NAMD 2 versions. See announce.txt for details regarding correctness issues in : eigenvector, orientationAngle, orientation, both coordNum and selfCoordNum with pairlist, and distanceZ with dynamic axis. We strongly encourage users of Colvars in ALL versions of NAMD to upgrade immediately to version 3.0.2. |
| NAMD 3.0 New Features - webpage is posted |
| NAMD GPU-resident benchmarks - results and data sets with GPU-optimized configuration posted |
| 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: Overcoming the Challenges of High-Resolution Data (September 2016)
image size:
3.3MB
made with VMD
Living cells are brimming with the activity of macromolecular complexes carrying out their assigned tasks. Structures of these complexes can be resolved with cryo-electron microscopy (cryo-EM), wherein the complexes are first freeze-shocked into states characterizing their action and subsequently imaged by detection cameras. Recent advances in direct detection camera technology enable today's cryo-EM laboratories to image the macromolecular complexes at high-resolution, giving us a better view of the cell than ever before. Computational techniques like molecular dynamics flexible fitting (MDFF) are a key tool for producing atomic models of the imaged molecules, providing greater insight into their structure and function. The increased resolution of EM maps, which contain sharp valleys capable of trapping structures, presents a challenge to MDFF which was originally developed for maps in a lower resolution range. However, a recent study unveils two new techniques called cascade (cMDFF) and resolution exchange (ReMDFF) molecular dynamics flexible fitting to overcome the hurdles posed by high-resolution maps. The refinement is achieved by interpreting a range of cryo-EM images, starting with an image of fuzzy resolution and progressively improving the image's contrast until near-atomic resolution is reached. These techniques were employed to solve the structure of the proteasome, the recycling machine of the human cell. New analysis schemes that look at the flexibility of the obtained structure provide a measure of model uncertainty within the near-atomic EM images, improving their contrast. All the tools are available on cloud computing platforms allowing community-wide usage at low monetary cost; the complex computations can now be performed at the cost of a cup of coffee.
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 3.0.2 Release (Aug 2025)
NAMD 3.0.1 Release (Oct 2024)
NAMD 3.0 Release (Jun 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
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
