Faculty for Chemistry and Pharmacy - Group of Prof. Zipse
LMU
Faculty
Dept. of Biochemistry
Dept. of Chemistry
Dept. of Pharmacy
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Computational Chemistry 1
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Force Field Calculation with TINKER
Research
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Teaching
Computational Chemistry 1
Topics
Getting Started with Linux
Basic UNIX commands
vi Editor
Ghostview
Cartesian Coordinates
PBS Queueing System
Gaussian Input Files
Running Gaussian Jobs on the CIP-Cluster
Gaussian Output Files
Molden
GaussView
Using Symmetry
Geometry Definition
Internal Coordinates
Redundant Internal Coordinates
Geometry Optimization - Basic Considerations
Newton-Raphson (NR) optimization
Comparative Examples
Transition State Searching
Scanning Potential Energy Surfaces
Eigenvector Following with the Berny Algorithm
Global Search Algorithms: STQN
Following the Intrinsic Reaction Coordinate
A Worked Example
Choosing a Coordinate System
Force Field Methods
Force Field Calculations in Gaussian 03
Force Field Calculation with TINKER
Files and Subprograms used by Tinker
Construction and Optimization of Peptides
Searching Conformational Space
Amino Acids and their Abbreviations
Combined Use with Other Programs
Vibrational Frequencies - Technical Considerations
Assigning Vibrational Frequencies
Vibrational Frequencies - Isotope Effects
Thermochemistry
Reaction Energetics
Arrhenius and Eyring equations
Hartree-Fock Theory - Basic Considerations
Treating Open Shell Systems
Convergence in Hartree-Fock Calculations
Stability of Wavefunctions
Performance in Hartree-Fock Calculations
Density Functional Theory
Semiempirical Methods
The MOPAC Program Package
The Basis Set Superposition Error (BSSE)
Information on Molecular Orbitals in the Gaussian output file
Visualization of Molecular Orbitals using MOLDEN
Visualization of Molecular Orbitals using GaussView
Population Analysis - where really are these electrons?
Mulliken Population Analysis
Natural Bond Orbital (NBO) Analysis
Molecular Electrostatic Potential (MEP)
Determining Atomic Charges using the CHELPG Scheme
Determining Atomic Charges using the Merz-Singh-Kollman (MK) Scheme
Atoms In Molecules
Pauling bond order
Information on Gaussian 03/09
Information on Tinker and FFE
Constants and Conversion Units
Monographs
Computational Chemistry Links
Computational Chemistry 2
Organische Chemie 5
Radicals in Chemistry and Biology
Organisch-chemisches Praktikum für Lehramtstudierende
Organische Chemie 1
RAMIOC
Internal Information
VidBibOCP-Videothek
Print
The Tinker Molecular Modeling Suite
Subprograms and files
used by Tinker
Building and optimzing peptides
Searching the conformational space
of macromolecules
Amino acids and their abbreviations
Combined use
with other programs