Molecular Dyamics

Contents

• Background
• Integration Algorithms
  • Introduction
  • Criteria of Good Integrators in Molecular Dynamics
  • Integrators in the Discover 2.9.5 and 95.0 Programs
    • Verlet Leapfrog Integrator
    • Verlet Velocity Integrator
    • ABM4 Integrator
    • Runge-Kutta-4 Integrator
• The Choice of Timestep
• Integration Errors
  • Example 1--Two Colliding Hydrogen Atoms
  • Example 2--Energy Conservation of a Harmonic Oscillator
• Stages and Duration of Dynamics Simulations
• Statistical Ensembles
  • Introduction
  • NVE Ensemble
  • NVT Ensemble
  • NPT Ensemble
  • NST Ensemble
  • NPH Ensemble
• Temperature
  • Introduction
  • How Temperature Is Calculated
  • How Temperature Is Controlled
    • Direct Velocity Scaling
    • Berendsen's Method of Temperature-Bath Coupling
  • Nosé Dynamics
  • Andersen Method
• Pressure and Stress
  • Introduction
  • Units and Sign Conventions
  • How Pressure is Calculated
  • How Pressure is Controlled
    • Berendsen Method of Pressure Control
    • Andersen Method of Pressure Control
    • Parrinello-Rahman Method of Pressure and Stress Control
• Constraints
• General Methodology
  • Main Uses of Dynamics Simulations
  • Exploring Conformational Space using Dynamics
    • Conformational Search of ANF using Dynamics and Minimization
    • Characterizing Vasopressin Dynamics

Main access page

Theory/Methodology access

Minimization References