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 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. For more information about the bugs in Colvars, please see Colvars Bugfix Announcement. We encourage all NAMD users to upgrade 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: Fighting the Flu using Computation (Dec 2012)
image size:
77.5KB
made with VMD
Did you get your flu shot this year? Influenza is a leading cause of preventable death in the industrialized world, representing hundreds of billions of dollars in healthcare expenditures and loss of economic production. While the yearly influenza vaccination is nearly 90% effective at limiting infections in populations less than 65 years of age, there is insufficient evidence regarding the effectiveness of the flu shot for the elderly population, whose immune systems may not mount an adequate antibody response to vaccination. Beyond vaccination, front-line therapies such as the neuraminidase inhibitors Tamiflu and Relenza have proven to be of limited effectiveness due to the evolution of drug-resistant influenza mutants. Therefore, a need exists for the development of new therapies to circumvent these resistance mechanisms. Computational biologists employing NAMD and VMD used molecular simulations to uncover the key role that water plays in mediating how well antiviral drugs can bind to proteins of the influenza virus. This investigation, reported recently, reveals that amino-acid mutations responsible for drug resistance act by reshaping the local electric field and also by permitting infiltration of water within the otherwise hydrophobic drug binding pocket. These mutations thus induce drug resistance in much the same way as inverting the polarity of a magnet can repel rather than attract. These findings are expected to help guide the design of novel drugs with increased antiviral efficacy. Additional details about this study 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 3.0.2 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
