Contents

• NAMD Molecular Dynamics Software
  Non-Exclusive, Non-Commercial Use License
• Contents
• List of Figures
• Introduction
  • New features in version 2.5b1
  • 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
  • AMBER force field parameters
  • GROMACS force field paramets
• Creating PSF Structure Files
  • Ordinary Usage
  • List of Commands
  • BPTI Example
  • Building solvent around a protein
• 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
  • Alchemical Free Energy Perturbation Calculations
  • Locally Enhanced Sampling
• Translation between NAMD and X-PLOR configuration parameters
• Sample configuration files
• Running NAMD
  • Individual Workstations
  • Individual Windows Workstations
  • Workstation Networks
  • Windows Workstation Networks
  • Scyld Beowulf Clusters
  • Compaq AlphaServer SC
  • IBM RS/6000 SP
  • Cray T3E
  • Origin 2000
• NAMD Availability and Installation
  • How to obtain NAMD
  • Platforms on which NAMD will currently run
  • Compiling NAMD
  • Documentation
• Bibliography
• About this document ...