Next: Preface Contents
OOPSE: An Object-Oriented Parallel Simulation Engine for Molecular Dynamics
Matthew A. Meineke, Charles F. Vardeman II, Teng Lin,
Christopher J. Fennell and J. Daniel Gezelter
Department of Chemistry and Biochemistry
University of Notre Dame
Notre Dame, IN 46556, USA
- 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
- 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
- Energy Minimization
- Parallel Simulation Implementation
- Conclusion
- Acknowledgments
- Bibliography
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Updated on January 16, 2006