Contents

• Contents
• List of Figures
• Introduction
  • New features in version 2.0
  • NAMD and molecular dynamics simulations
  • User feedback
  • Acknowledgments
• Getting Started
  • What is needed
  • NAMD configuration file
• Input and Output Files
  • File formats
  • NAMD configuration parameters
• Basic Simulation Parameters
  • Non-bonded interaction parameters and computations
  • Full electrostatic integration
  • NAMD configuration parameters
• Additional Simulation Parameters
  • Constraints and Restraints
  • Energy Minimization
  • Temperature Control and Equilibration
  • Boundary Conditions
  • Pressure Control
  • Applied Forces and Analysis
  • Free Energy of Conformational Change Calculations
• Translation between NAMD and X-PLOR configuration parameters
• Sample configuration files
• Running NAMD
  • Platform-Specific Notes
  • Interactive modeling with MDScope
• NAMD Availability and Installation
  • How to obtain NAMD
  • Platforms on which NAMD will currently run
  • Compiling NAMD
  • Documentation
• Bibliography