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

Other Spotlights 

image size: 1.9MB
Olga Svinarski and VMD

The molecular graphics program VMD has evolved to version 1.9, featuring new and improved tools for molecular cell biology. A key new tool in VMD permits visual diagnosis of the long-time dynamics of large structures. Improved computer power permits now simulation of processes like protein folding that stretch over microseconds to milliseconds. While short in human time, the process measured in terms of basic molecular motion like bond vibration is seemingly endless, involving hundreds of gigabytes of data and long hours of human attention, if not automated. VMD offers now with the Timeline tool, a convenient way of scanning such data for key "events" that signal successful process steps. Timeline can likewise assist in monitoring the dynamics of large cellular machines involving millions of atoms. VMD 1.9 sports other new tools like ParseFEP for analyzing so-called free energy perturbation calculations determining the energy arising in reaction processes as calculated with VMD's sister program NAMD. VMD includes now also a lightening fast tool to detect spatial regularities in the arrangement of small molecules in order to detect if they constitute disordered or ordered arrangements. By calculating the so-called radial distribution function the tool could identify plug formation in nanopore sensors due to precipitates that go undetected by density or visual inspection. Pleasing to the eye, molecular graphics features in VMD have been enhanced, enabling faster ray tracing, new shading features, X3D molecular scene export for display in WebGL-capable browsers including Chrome, Firefox, and Safari. See more on the VMD 1.9 release page.

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

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