Proposed Topics

Sample input files and configuration scripts for all exercises are found in the tutoral directory.

Electronic Structure Calculations

  1. Potential Energy Surfaces and Reaction Pathways

    Building Molecules, Symmetry Concepts and Group Theory

    Hartree-Fock and Density Functional Methods

    Rotational Barriers, Conformational Analysis, Geometry Optimization, Frequency Analysis, Transition States, Charge and Overlap Population Analysis

    Reactivity of Molecules, Statistical Thermodynamics, Free Energy Calculations, Bond Strengths, Dissociation Energies, Kinetic Isotope Effect

  2. Molecular Spectroscopy

    IR, UV, NMR, and other spectroscopic methods

In the above exercises, Gaussian, ORCA, GAMESS, and perhaps NWChem will be used.

Molecular Dynamics Simulations

The Molecular Mechanics Force Field and Molecular Dynamics methods will be discussed followed by several exercises.
  2. NAMD

Advanced Topics

  1. LAMMPS: exploration of Molecular Dynamics simulations for polymer and materials systems.
  2. NAMD: continuation of a Protein-Ligand Complex simulation started with CHARMM

    This is an illustration of a possible pathway for proceeding with a Molecular Dynamics Simulation.

    CHARMM was used above to initially set up a solvated protein-ligand system, followed by shorter simulations for equilibration. This simulation will contine with longer production runs using NAMD.

    NAMD DCD trajectory files can be both visualized and analyzed with VMD using Tcl script files. DCD files are fully compatible with CHARMM and can also be used for trajectory analysis.

  3. Gaussian (ONIOM) and Hybrid QM/MM NAMD: Quantum Mechanics/Molecular Mechanics (QM/MM) calculations using both these methods will be performed.

    These methods extend the ability of simulations to provide more realistic models for experiments.

    NAMD is especially well-suited for carrying out long simulations of combined Quantum Mechanics / Molecular Mechanics systems, because of its good parallel scaling ability.