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Quantum Chemistry III
 

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 Quantum Chemistry III Presentation Transcript

    • Quantum Mechanics Calculations III
      Noel M. O’Boyle
      Apr 2010
      Postgrad course on Comp Chem
    • Overview of QM methods
      Molecular mechanics
      Quantum mechanics
      (wavefunction)
      Quantum mechanics
      (electron density)
      Including correlation
      HF (“ab initio”)
      Semi-empirical
      DFT
      Speed/Accuracy
      Forcefields
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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)