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Erasmus Mundus

Molecular Design
Przemysław Dopieralski, Ph.D.

  • 5th APRIL 2017
  • 12th APRIL 2017
  • 26st APRIL 2017
  • 10th MAY 2017

  • This course is based on four different softwares:

    • HyperChem

      HyperChem Release 8.0 is the newest Windows member of the HyperChem Family. Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods, as well as density functional theory. HyperChem Data and HyperNMR are included as part of HyperChem. New features are continually added and include elegant Open GL rendering, TNDO, RM1, Charmm protein simulations, molecules in magnetic fields, interfaces to third-party applications, calculations of structure, spectra, rate constants and much more. HyperChem is applicable to macromolecules as well as small molecules and is scriptable.

    • Gaussian

      Gaussian 09 is the latest version of the Gaussian® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures). Gaussian

    • Gamess

      GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the polarizable Continuum Model. Numerous relativistic computations are available, including third order Douglas-Kroll scalar corrections, and various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code. GAMESS

    • Car-Parrinello Molecular Dynamics

      The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Its first version was developed by Jurg Hutter at IBM Zurich Research Laboratory starting from the original Car-Parrinello codes.
      CPMD main characteristics
      * works with norm conserving or ultrasoft pseudopotentials
      * LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
      * isolated systems and system with periodic boundary conditions; k-points
      * molecular and crystal symmetry
      * wavefunction optimization: direct minimization and diagonalization
      * geometry optimization: local optimization and simulated annealing
      * molecular dynamics: constant energy, constant temperature and constant pressure
      * path integral MD
      * response functions
      * excited states
      * many electronic properties
      * time-dependent DFT (excitations, molecular dynamics in excited states)
      * coarse-grained non-Markovian metadynamics



    Laboratory 1 Starting with HyperChem PDF Hyperchem Home page:
    Laboratory 2 Practical use of HyperChem - H2O, NH3, alanine PDF
    Laboratory 3 Practical use of HyperChem - HEM B PDF
    Laboratory 4 Gaussian - Introduction and something more      PDF Gaussian home page:
    Basic introduction to vi editor under Linux     PDF
    Laboratory 5 Car-Parrinello Molecular Dynamics      PDF Car-Parrinello Molecular Dynamics Home page:
    Nice Tutorial by Axel Kohlmeyer:    TUTOR-PDF
    All needed input files for Tutorial:    INPUTS-PDF
    After downloading change the name of the file cpmd-tutor-inputs.txt for cpmd-tutor-inputs.tar.gz