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OOPSE: An Object-Oriented Parallel
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Preface
Contents
List of Figures
List of Tables
Introduction
Concepts & Files
Meta-data Files
Atoms, Molecules, and other ways of grouping atoms
Creating a Metadata File
Coordinate Files
Generation of Initial Coordinates
The Statistics File
The Empirical Energy Functions
The Lennard Jones Force Field
Dipolar Unified-Atom Force Field
DUFF Energy Functions
The DUFF Water Models: SSD/E and SSD/RF
The WATER Force Field
Embedded Atom Method
Periodic Boundary Conditions
Mechanics
Integrating the Equations of Motion: the DLM method
Extended Systems for other Ensembles
Nosé-Hoover Thermostatting
Constant-pressure integration with isotropic box deformations (NPTi)
Constant-pressure integration with a flexible box (NPTf)
Constant pressure in 3 axes (NPTxyz)
Constraint Methods
The RATTLE Method for Bond Constraints
The Z-Constraint Method
Energy Minimization
Parallel Simulation Implementation
Conclusion
Acknowledgments
Bibliography
Copyright © 2006
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University of Notre Dame
Updated on January 16, 2006