Quantum Chemistry III
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University College Cork Lecture Series on Computational Chemistry - Lecture 3

University College Cork Lecture Series on Computational Chemistry - Lecture 3

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Quantum Chemistry III Presentation Transcript

  • 1. Quantum Mechanics Calculations III
    Noel M. O’Boyle
    Apr 2010
    Postgrad course on Comp Chem
  • 2. Overview of QM methods
    Molecular mechanics
    Quantum mechanics
    (wavefunction)
    Quantum mechanics
    (electron density)
    Including correlation
    HF (“ab initio”)
    Semi-empirical
    DFT
    Speed/Accuracy
    Forcefields
  • 3. Carrying out calculations
    http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software
    Gaussian (commercial)
    The most widely used package
    Can do most everything, and is pretty robust. Presumably not the fastest (the only software whose license prohibits published comparisons).
    Gaussian09 available through ICHEC, also faster (8-CPU machines)
    ORCA (free for academics)
    General purpose
    http://www.thch.uni-bonn.de/tc/orca/
    Lots of other commercial packages: ADF (for DFT), Jaguar
    MOPAC2009 (commercial but free for academics)
    Semi-empirical calculations, Stewart
    NWChem (free for academics)
    General purpose
    http://www.emsl.pnl.gov/capabilities/computing/nwchem/
    GAMESS (available for free)
    General purpose calculations. (See next page)
    Firefly
    Fork of GAMESS, formerly “PC GAMESS”
    Faster than GAMESS (especially on Windows)
    PSI3 (Open Source)
    HF and higher level
    http://www.psicode.org/, no Windows support
  • 4. Once you have the QM software...
    Set up calculations
    Avogadro (OS, http://avogadro.sf.net)
    GaussView (commercial, available when buying Gaussian)
    Analyse results
    Avogadro
    Molekel (OS, http://molekel.cscs.ch)
    GaussSum (OS, http://gausssum.sf.net, by me)
    MacMolPlt (free, http://www.scl.ameslab.gov/MacMolPlt/)
    ...and many others
  • 5. Get GAMESS
    GAMESS is free (but not open-source) software developed by the Gordon Group and collaborators
    To get it...
    Go to http://www.msg.ameslab.gov/GAMESS/
    Click on “How to get GAMESS”
    Click “Obtaining GAMESS”
    Click “I agree”
    Enter email address, and tick box for “GAMESS version January 12, 2009 R3 for Microsoft Windows” (also a ChemOffice version – haven’t tried it)
    Click “Submit request”
    You will receive an email with a link, and a username and password
    Follow the link to download the installer and enter the username and password when requested
    To install it...
    Run the installer
    Click Next a few times
    It installs to C:WinGAMESS
    To use it...
    Documentation is in C:WinGAMESSmanuals
    Following C:WinGAMESSmanualsWinGAMESS.pdf we can...
    Create a shortcut to C:WinGAMESSWG_DDE.bat on the desktop
    Drag-and-drop GAMESS input files onto this shortcut
    How do we create an input file?
    Install Avogadro and MacMolPlt
  • 6. Input for a calculation
    What type of calculation to do
    Location and atomic number of atoms
    Charge on molecule
    Multiplicity of molecule
    No need for bond orders
    No need to say where the charge is
    The charge is simply used to calculate the total number of electrons
    Typical calculations are in vacuo
    i.e. not in solid or liquid state, or in solvent
    If required, there is software for handling bulk solids, and there are methods to include solvent effects
  • 7. Jan Jensen’s GAMESS Screencasts
    http://molecularmodelingbasics.blogspot.com/
    Look at all of Jan’s screencasts and posts starting from the oldest
    On the right-hand side, see under Blog Archive
    Tools of the trade (all free, some open source)
    http://molecularmodelingbasics.blogspot.com/2009/06/tools-of-trade.html
    Building a molecule
    http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-2d-to-3d.html
    Finding the lowest energy conformer
    http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-and.html
    Look at the GAMESS input file
    http://molecularmodelingbasics.blogspot.com/2009/07/some-gamess-input-basics_24.html
    Set up a calculation using Avogadro
    http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html
    Finding a transition state
    http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2-reaction.html
    Finding the path connecting reactant to product (intrinsic reaction coordinate)
    http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html
  • 8. Practical tips
    To speed up a geometry optimization, you can optimise first with a smaller basis set and then continue from there
    If you have trouble with SCF convergence, it can be a good idea to try converging it with a smaller basis set first and then projecting from that as the initial guess
    Molecules with geometrical symmetry will be corresponding faster (on the other hand, if you require symmetry to be broken during the calculation, you should turn off symmetry perception)