Inhalt

• Inhalt
• Abbildungsverzeichnis
• Tabellenverzeichnis
• Introduction
  • What is EGO?
  • What to Read
  • Hardware & Software Requirements
  • For Further Information
• Getting Started - Computing a Trajectory
  • Installing EGO on Your Computer
  • Preparing Simulation Data for EGO
  • Creating lis-files for EGO
  • Setting the Control Parameters
  • Running EGO
  • EGO Output
  • Data Analysis
  • Summary
• Starting and stopping EGO
• The Control File
  • List of lis-files
  • Requested Number of Nodes
  • Frequency of Analysis Printout
  • Frequency of Writing Restart-file
  • Frequency of System Call
  • Frequency of Energy Printout
  • Number of Integration Steps
  • Integration Time Step
  • Order of Exclusion List
  • Switch for Minimisation
  • Switch for Equilibration
  • Number of Distance Classes
  • Used Type of Cluster Algorithm
  • Number of Hierarchy Levels
  • Number of Branches on Last Level
  • Step for New Clustering
  • Path for Output Data
  • 1-4 Electrostatic Damping
  • Switch for Stochastic Boundary
  • Switch for Harmonic Restraints
  • Switch for SHAKE on Hydrogens
  • Definition of SBOUND Region
  • Maximum Friction Coefficient
  • Switch for Using Flooding
  • Switch for Using Translation and Rotation Correction
  • Switch for Using Adaptive Flooding
  • Initial Energy for Flooding in kT
  • Final Energy for Flooding in kT
  • Flooding energy increase in kT/ps
  • Time constant for adaptive flooding in s
  • Number of User Defined Integers and Doubles
  • Switch for using immobilisation
  • Pulling and stepping mode
  • The Free Format Section
    • Control of force output
    • Control of minimization
    • Control of constraints
    • Calculation of the Hesse-Matrix
• Implementation
  • Structure of EGO
  • Structure of xpl2lis
• Methods
  • Numerical Tasks in Molecular Dynamics Simulations
    • Energy Function
    • Integration Methods
  • Methods to Increase Efficiency
    • Distance Cut-Off Scheme
    • Multiple Time Step Method
    • Structure Adapted Multipole Method
    • Fast Multiple Time Step Structure Adapted Multipole Method
    • Conformational Flooding
• File Formats
  • Input Files
    • The units definition file units.def
    • Brookhaven PDB Atom Coordinate Files
    • X-PLOR Protein Structure Files (PSF)
    • X-PLOR Parameter Files
    • X-PLOR Topology Files
  • Output Files
    • EGO Trajectory Output Files (.ego)
    • X-PLOR Trajectory Files (.DCD, .crd)
    • EGO Energy Summary Files (.eny)
    • Format of the `flooding' matrix file flooding.lis
• Comparison of EGO and X-PLOR
  • Important differences between EGO and X-PLOR
  • Common features of EGO and X-PLOR
  • Features Unique to EGO
• References
  • Molecular Dynamics
• Literatur