Contents

• NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License
• List of Figures
• Introduction
  • NAMD and molecular dynamics simulations
  • Acknowledgments
  
  
• Getting Started
  • What is needed
  • NAMD configuration file
  
  
• Input and Output Files
  • File formats
  • NAMD configuration parameters
  • AMBER file and force field support
  • GROMACS file support
  
  
• Creating PSF Structure Files
  • New commands and Functionalities
  • Ordinary Usage
  • BPTI Example
  • Building solvent around a protein
  • New Commands in the version 2.0
  • List of Commands
  • Example of a Session Log
  
  
• Force Field Parameters
  • Potential energy functions
  • Non-bonded interactions
  • Water Models
  • Drude polarizable force field
  • MARTINI Residue-Based Coarse-Grain Forcefield
  • Constraints and Restraints
  
  
• Generalized Born Implicit Solvent
  • Theoretical Background
  • 3-Phase Calculation
  • Configuration Parameters
  
  
• Standard Minimization and Dynamics Parameters
  • Boundary Conditions
  • Energy Minimization
  • Dynamics
  • Temperature Control and Equilibration
  • Pressure Control
  
  
• User Defined Forces
  • Constant Forces
  • External Electric Field
  • Grid Forces
  • Moving Constraints
  • Rotating Constraints
  • Symmetry Restraints
  • Targeted Molecular Dynamics (TMD)
  • Steered Molecular Dynamics (SMD)
  • Interactive Molecular Dynamics (IMD)
  • Tcl Forces and Analysis
  • Tcl Boundary Forces
  • External Program Forces
  
  
• Collective Variable-based Calculations (Colvars)
  • Overview
  • Writing a Colvars configuration: a crash course
  • Enabling and controlling the Colvars module in NAMD
  • Defining collective variables
  • Selecting atoms
  • Biasing and analysis methods
  • Scripting interface (Tcl): list of commands
  • Syntax changes from older versions
  
  
• Alchemical Free Energy Methods¹
  • Theoretical Background
  • Implementation of the free energy methods in NAMD
  • Examples of input files for running alchemical free energy calculations
  • Description of a free energy calculation output
  • Hybrid single-dual topology approach for relative binding free energy calculation of ligand to receptor
  
  
• Accelerated Sampling Methods
  • Accelerated Molecular Dynamics
  • Gaussian Accelerated Molecular Dynamics
  • Solute Scaling and REST2
  • Adaptive Tempering
  • Locally enhanced sampling
  • Replica exchange simulations
  • Random acceleration molecular dynamics simulations
  
  
• Structure based simulations
  • Hybrid MD-Go Simulation
  • Running SMOG simulations
  
  
• Constant-pH Simulations ¹
  • Overview and Theoretical Background
  • Implementation Details
  • New Commands and Keywords
  • Minimal Examples
  
  
• Hybrid QM/MM Simulations
  • Division of Labor
  • Mechanical and Electrostatic Embedding
  • Covalent Bonds Divided by the QM/MM Barrier
  • Custom Quantum Chemistry Software
  • Independent QM Regions
  • Keywords
  
  
• Runtime Analysis
  • Pair interaction calculations
  • Pressure profile calculations
  
  
• Performance Tuning
  • NAMD performance tuning concepts
  • Non-bonded interaction distance-testing
  
  
• Translation between NAMD and X-PLOR configuration parameters
• Sample configuration files
• Running NAMD
  • Individual Windows, Linux, Mac OS X, or Other Unix Workstations
  • Windows Clusters and Workstation Networks
  • Linux Clusters with InfiniBand or Other High-Performance Networks
  • Linux or Other Unix Workstation Networks
  • Shared-Memory and Network-Based Parallelism (SMP Builds)
  • Cray XE/XK/XC
  • Xeon Phi Processors (KNL)
  • SGI Altix UV
  • IBM POWER Clusters
  • CPU Affinity
  • CUDA GPU Acceleration
  • Xeon Phi Acceleration
  • Memory Usage
  • Improving Parallel Scaling
  
  
• NAMD Availability and Installation
  • How to obtain NAMD
  • Platforms on which NAMD will currently run
  • Installing NAMD
  • Compiling NAMD
  • Documentation
  
  
• Bibliography
• Index
• About this document ...