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.

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made with VMD

The Golgi apparatus found in so-called eukaryotic cells acts like Amazon.com, namely accepting delivery of newly synthesized proteins, packaging them, and sending them out. However, in comparison to Amazon.com the Golgi apparatus uses immensely more advanced packaging materials made of a multitude of lipids. The various lipids form membranes in the shape of vesicles. Depending on lipid type specific goods are packaged inside the vesicles, specific locations in the cell receive the packages, content is emptied there and packages are retrieved. To achieve the series of steps just outlined, lipids as the main actors need to be coordinated. One way is to recognize lipids forming vesicle membranes and to modify them to be readied for a subsequent step, for example going from release step to retrieval step. For this purpose eukaryotic cells engage a special class of proteins, named kinases, that can recognize membrane lipids and phosphorylate them, adding a so-called phosphate group. As reported recently, a team of experimental and computational scientists determined the atomic structure of a key member in the kinase family, phosphatidylinositol 4-kinase (PI4K). The scientists discovered not only the structure, but also how PI4K captures and phosphorylates a particular type of lipid molecule, thereby changing a vesicular membrane and turning on the next step in the cellular package delivery system. The discoveries, made possible through the software NAMD and VMD, are expected to have an impact on the design of novel drugs that suppress cancer cell growth. More on our kinase 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

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