Contents

• Contents
• List of Figures
• Introduction
  • New features in version 1.5
  • New features in version 1.4
  • NAMD and molecular dynamics simulations
  • User feedback
  • Acknowledgments
• Installing and Running
  • Obtaining NAMD
  • Supported platforms
  • Required packages
  • Optional packages
  • Compiling and installing NAMD
  • Running NAMD simulations
  • Testing NAMD
• Molecular Input and Output File Formats
  • PDB files
  • X-PLOR format PSF files
  • CHARMm19 and CHARMm22 parameter files
  • DCD trajectory files
• NAMD Configuration File
  • Configuration parameter syntax
  • NAMD configuration parameters
  • Translation between NAMD and X-PLOR configuration parameters
  • Sample configuration files
  • Non-bonded interaction parameters and computations
• Computational Details
  • Force fields
  • Integration
  • Units, constants, and conversion factors
• Bibliography