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 3.0.1 Release - Point release bug fixes for stable release 3.0 featuring new GPU-resident mode for NVIDIA and compatible AMD GPUs. Updates to Colvars, Charm++, and user guide documentation. We strongly encourage users of version 3.0 to upgrade immediately to version 3.0.1. |
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: Water, Water, Everywhere (Dec 2011)
image size:
573.0KB
Olga Svinarski and VMD
Water is ubiquitous; living cells and the cells' biomolecules are greatly influenced by water. Accounting for water in computational modeling, a key access route to imaging cell processes, comes at a stiff price: up to 90% of the simulation volume needs to be a water bath embedding simulated biomolecular machinery. The sheer number of water molecules arising here, sometimes millions, and the strong hydrodynamic drag resisting biomolecular dynamics, slows down simulations tremendously. Computational biologists had invented a means to replace water by a kind of continuous ether, so-called implicit solvent, that accounts for key electrostatic features of water around biomolecules, but does not slow down simulations. Computational hinderance through explicit water is getting worse with increasing size of biomolecular machines, but so far the implicit solvent description could not be effectively employed to model large systems using supercomputers. In a recent study, the situation has been repaired and the use of an implicit solvent in molecular dynamics simulations of systems as large as the whole ribosome (containing 300,000 ribosome atoms and eliminating 2,700,000 water atoms) have been documented. In a further study, the implicit solvent description has been extended to account also for hydrophobic interactions at biomolecular surfaces; the extension took advantage of delegating calculations both to GPU and CPU as the latter is more suitable for the evaluation of surface interactions. More information regarding NAMD's parallel computer-ready implicit solvent can be obtained from the NAMD 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 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