Molecular Dynamics

  Molecular dynamics consists of solving Newton's equations of motion 

where the index i runs through all free (i.e., not fixed) atoms and the gradient is derived from the X-PLOR energy function (Chapter 4). Presently, X-PLOR provides the option to solve Eq. 10.1 in Cartesian coordinate space (Section 10.1) or rigid-body coordinate space (Section 10.2). Molecular dynamics simulations can be stored as trajectory files. Input format, output format, manipulations, and analysis of trajectory files are described in Section 10.

• Cartesian Coordinate Space
  • Simple Langevin Dynamics
  • Velocity Assignment
  • Temperature Control
    • Velocity Rescaling
    • Langevin Dynamics
    • Temperature Coupling
  • Finite Difference Approximation
  • Dynamics Restarts
  • Syntax of the Dynamics Verlet Statement
  • Requirements
  • Example: Run a Standard Molecular Dynamics Simulation
  • Example: Run a Molecular Dynamics Simulation with Temperature Coupling
  • Example: Run a Slow-cooling Molecular Dynamics Simulation
  • Example: Run Langevin Dynamics
• Rigid-Body Coordinate Space
  • Initialization
  • Iteration
  • Syntax of the Dynamics Rigid Statement
  • Requirements
  • Example: Run a Rigid-Body Dynamics Simulation