Chapter 5
Calculation of Molecular Structure and Ab Initio Molecular Dynamics

 5.1 Structure Optimizations using the JOBEX Script
  5.1.1 Options
  5.1.2 Output
 5.2 Program STATPT
  5.2.1 General Information
  5.2.2 Hessian matrix
  5.2.3 Finding Minima
  5.2.4 Finding transition states
 5.3 Program Relax
  5.3.1 Purpose
  5.3.2 Optimization of General Coordinates
  5.3.3 Force Constant Update Algorithms
  5.3.4 Definition of Internal Coordinates
  5.3.5 Structure Optimizations Using Internal Coordinates
  5.3.6 Structure Optimization in Cartesian Coordinates
  5.3.7 Optimization of Basis Sets (SCF only)
  5.3.8 Simultaneous Optimization of Basis Set and Structure
  5.3.9 Optimization of Structure and a Global Scaling Factor
  5.3.10 Conversion from Internal to Cartesian Coordinates
  5.3.11 Conversion of Cartesian Coordinates, Gradients and Force Constants to Internals
  5.3.12 The m-Matrix
  5.3.13 Initialization of Force Constant Matrices
  5.3.14 Look at Results
 5.4 Force Field Calculations
  5.4.1 Purpose
  5.4.2 How to Perform a UFF Calculation
  5.4.3 The UFF implementation
 5.5 Molecular Dynamics Calculations
 5.6 Counterpoise-Corrections using the JOBBSSE Script
  5.6.1 Options
  5.6.2 Output
 5.7 Reaction Path Optimization
  5.7.1 Background and Program structure
  5.7.2 Input Structure
  5.7.3 How it works