Laboratory
Przemysław Dopieralski, Ph.D.
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 semiempirical and abinitio 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 thirdparty applications, calculations of structure, spectra, rate constants and much more. HyperChem is applicable to macromolecules as well as small molecules and is scriptable. www.hyper.com
 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., shortlived 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 CoupledCluster 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 DouglasKroll scalar corrections, and various spinorbit 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
 CarParrinello Molecular Dynamics
The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for abinitio molecular dynamics. Its first version was developed by Jurg Hutter at IBM Zurich Research Laboratory starting from the original CarParrinello 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; kpoints
* 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
* timedependent DFT (excitations, molecular dynamics in excited states)
* coarsegrained nonMarkovian metadynamics
CPMD
Instructions:
Laboratory 1  Starting with HyperChem  Hyperchem Home page: www.hyper.com  
Laboratory 2  Practical use of HyperChem  H_{2}O, NH_{3}, alanine  
Laboratory 3  Practical use of HyperChem  HEM B  
Laboratory 4  Gaussian  Introduction and something more 
Gaussian home page: www.gaussian.com Basic introduction to vi editor under Linux PDF 

Laboratory 5  CarParrinello Molecular Dynamics 
CarParrinello Molecular Dynamics Home page: www.cpmd.org Nice Tutorial by Axel Kohlmeyer: TUTORPDF All needed input files for Tutorial: INPUTSPDF After downloading change the name of the file cpmdtutorinputs.txt for cpmdtutorinputs.tar.gz 