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 Release - Stable release featuring new GPU-resident mode for NVIDIA and compatible AMD GPUs. Updates to Colvars, Charm++, and user guide documentation. |
| 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: Managing the Protein Assembly Line (Dec 2009)
Living cells contain millions of proteins composed of sequences of different amino acids that typically fold spontaneously into well-defined three-dimensional conformations and then carry out their role as molecular machines serving manifold functions in the cells (see the protein folding highlight). The synthesis of the proteins is carried out by the ribosome, one of the largest molecular machines present in all cells, which reads the cell's genetic information for the purpose. Three researchers were recently awarded the 2009 Nobel Prize in Chemistry for the determination of the ribosome's structure. The physical mechanism of the ribosome, the cell's protein factory, is still largely unknown. Just as in any factory, there are multiple directions and controls on the protein assembly line. Sometimes the protein products need to be redirected to different parts of the cell, and other times assembly needs to be halted altogether. Now, significant new insights into both of these aspects of protein assembly have been made by combining electron microscopy with molecular dynamics simulations using the recently developed molecular dynamics flexible fitting method (MDFF, see the June 2008 highlight). This combination allowed researchers to visualize the complex between the ribosome and a protein-conducting channel that directs proteins into and across membranes for both a mammalian system (reported here) and a bacterial system (reported here). Amazingly, despite the evolutionary distance between mammals and bacteria, both complexes are remarkably similar. Simulations of the bacterial ribosome-channel complex, among the largest ever performed, further revealed the steps in the direction process. In a third study (reported here), researchers determined how TnaC, as a protein newly synthesized by the ribosome, can stall the ribosome from within during its own assembly, which then controls the expression of related genes. More information on these unique protein assembly controls can be found on our ribosome and our protein-conducting channel websites.
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 Release (June 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
