• FRONT MATTER
  • Title and Copyright Page
  • Acknowledgements
  • Abstract
  • List of Figures
  • List of Tables
• Chapter 1. Introduction
• PART I -- THEORY
  • Chapter 2. Molecular Mechanics and Dynamics
    • 2.1. Introduction
    • 2.2. Forcefields
    • 2.3. Microcanonical Dynamics
    • 2.4. Canonical Dynamics
    • 2.4. Minimization
  • Chapter 3. Cell Multipole Method
    • 3.1. Introduction
    • 3.2. Octree Decomposition
    • 3.3. Multipole Expansions
    • 3.4. Choice of Expansion Centers
    • 3.5. Combination of Multipoles
    • 3.6. Taylor Series Expansions
    • 3.7. Computation of Taylor Series Coefficients
    • 3.8. Farfield Evaluation and Nearfield Computation
  • Chapter 4. Reduced Cell Multipole Method
    • 4.1. Introduction
    • 4.2. Enhanced Multipoles
    • 4.3. Ewald Summation
    • 4.4. Exclusion of Neighbors
    • 4.5. Combination with CMM
    • 4.6. Noncubic Unit Cells
• PART II -- DESIGN AND IMPLEMENTATION
  • Chapter 5. Implementation on KSR
    • 5.1. Introduction
    • 5.2. KSR Architecture
    • 5.3. Memory
    • 5.4. Data Structures
    • 5.5. Modularity
    • 5.6. Features
      • 5.6.1. Coordinate Transformations
      • 5.6.2. Moving Atoms
      • 5.6.3. PBC Displacement Updating
      • 5.6.4. Atom Tracking
      • 5.6.5. General Valence Forcefield
      • 5.6.6. Nonbond Exclusions
      • 5.6.7. Spline Nonbonds
      • 5.6.8. Hydrogen Bonds and Off-Diagonal Nonbonds
      • 5.6.9. Initial Velocities
      • 5.6.10. Rigid Molecules
      • 5.6.11. Perturbation Thermodynamics
    • 5.7. Input/Output
    • 5.8. Parallelization
    • 5.9. Communications
    • 5.10. Dynamic Load Balancing
    • 5.11. Avoiding Synchronization
  • Chapter 6. Implementation on Message Passing Architectures
    • 6.1. Introduction
    • 6.2. Message Types
    • 6.3. Active Messages
    • 6.4. Load Balancing
    • 6.5. Input/Output
    • 6.6. Data Structures
    • 6.7. Computational Routines
  • Chapter 7. Performance
    • 7.1. Introduction
    • 7.2. Accuracy
    • 7.3. Timing
    • 7.4. Scalability
• PART III -- APPLICATIONS
  • Chapter 8. TVN Dynamics
    • 8.1. Introduction
    • 8.2. Procedure
    • 8.3. Results
    • 8.4. Conclusions
  • Chapter 9. Argon Clusters
    • 9.1. Introduction
    • 9.2. Procedure
    • 9.3. Results
    • 9.4. Conclusions
  • Chapter 10. Surface Tension of Liquid H2O and H2O on PTFE
    • 10.1. Introduction
    • 10.2. Drop Procedure
    • 10.3. Drop Results
    • 10.4. PTFE Simulation
    • 10.5. Procedure
    • 10.6. Results
    • 10.7. PTFE Surface Procedure
    • 10.8. PTFE Surface Results
    • 10.9. Conclusions
  • Chapter 11. Diffusion of Gases through Polymers
    • 11.1. Introduction
    • 11.2. Procedure
    • 11.3. Results
    • 11.4. Conclusions
  • Chapter 12. Viruses
    • 12.1. Introduction
    • 12.2. Procedure
    • 12.3. Results
    • 12.4. Conclusions