NAMD Tutorials

The tutorials below focus on NAMD-specific features, although many other tutorials utilize NAMD as well. Be sure you have the latest version of NAMD.

NAMD Tutorial
(html for Unix/Mac) (pdf for Unix/Mac, 8.3M)
(html for Windows) (pdf for Windows, 6.8M)
(required tutorial files (all platforms) [.tar.gz, 155M], [.zip, 155M], individual files (all platforms))
Participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files, with an emphasis on such files for protein energy minimization and equilibration in water. Tutorial versions available for Windows, or Mac and Unix/Linux platforms.

NAMD Paper
The physical concepts behind NAMD along with the programs design and algorithms are described in this publication that we recommend highly for study along with working through the above NAMD tutorial: Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005. Download full text: PDF ( 977k)
User-Defined Forces in NAMD (html) (pdf, 4.3M ) (required tutorial files [.tar.gz, 306M], [.zip, 306M], individual files)
This tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts. These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions. Tutorial works on Windows, Mac, and Unix/Linux platforms.

GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis (pdf, 443K) (required tutorial files [.tar.gz, 1.32GB]*)
This tutorial will demonstrate how to use features in NAMD and VMD to harness the computational power of graphics processing units (GPUs) to accelerate simulation, visualization and analysis. Requries VMD, NAMD. Works on Windows, Mac, and Linux. *Note: download of files may be limited by bandwidth availability.

Interactive Molecular Dynamics Tutorials

For a brief introduction to running interactive molecular dynamics simulations, see the documentation here. The tutorials on Simulation of Water Permeation through Nanotubes and on Stretching Deca-Alanine both utilize IMD.

Steered Molecular Dynamics Tutorials

Please also see the NAMD Tutorial, the Stretching Deca-Alanine tutorial, and the Forcing Substrates Through Channels tutorial for content on steered molecular dynamics.

Video Lecture

A video reviewing the conceptual foundations of NAMD, "Statistical Mechanics of Proteins" as recorded by Dr. Klaus Schulten in November 2010 is available here.