Utilities

In this section, the scripts used for MD analysis will be introduced. The insertion of the molecules in metal organic framework, the averaging of the atomic density distribution (ADD), and the determination of water network from MD trajectory.

Contents:

• Molecule insertion
  • Input
  • Example
• Atomic Density Distribution (ADD)
  • Formulation
  • Input
  • Example
    • The averaged ADD
    • The symmetrized ADD
    • The atomic-type decomposed ADD
    • The velocity-deconvoluted ADD
    • The energy-deconvoluted ADD
    • The derivative of ADD
    • The ADD on fixed equivalent positions
• Water network analysis
  • Input
  • Example